RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3968
(1080 letters)
>gnl|CDD|237263 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
Length = 1146
Score = 798 bits (2065), Expect = 0.0
Identities = 283/467 (60%), Positives = 347/467 (74%), Gaps = 10/467 (2%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
+HR KADE+YL+G+G PV AYL+I EIIRVAK+ VDAIHPGYGFLSE +FA+A +A
Sbjct: 43 LHRFKADEAYLIGEGKHPVRAYLDIDEIIRVAKQAGVDAIHPGYGFLSENPEFARACAEA 102
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFK 122
GI FIGP+ V++ +GDKVAAR AAI +GVP++PG+ GPI EEA+EF + G P++ K
Sbjct: 103 GITFIGPTAEVLRLLGDKVAARNAAIKAGVPVIPGSEGPIDDIEEALEFAEEIGYPIMLK 162
Query: 123 AAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKA 182
A+ GGGGRGMR+VR E++EE F+RA EAKAAFGN +++EK++E PRHIEVQ+LGDK
Sbjct: 163 ASAGGGGRGMRIVRSEEELEEAFERAKREAKAAFGNDEVYLEKYVENPRHIEVQILGDKH 222
Query: 183 GNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLC 242
GNVVHLYERDCSVQRRHQKVVEIAPAP L +R ++ + AVKLA+ VGY NAGTVEFL
Sbjct: 223 GNVVHLYERDCSVQRRHQKVVEIAPAPGLSEELRERICEAAVKLARAVGYVNAGTVEFLV 282
Query: 243 DESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELG---LTQEKISPQG 299
D G FYFIEVN R+QVEHTVTEE+TG+D+VQSQI +AEG TL +L +QE I +G
Sbjct: 283 DADGNFYFIEVNPRIQVEHTVTEEVTGIDIVQSQILIAEGATLHDLEIGIPSQEDIRLRG 342
Query: 300 FAIQCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIA 359
+AIQCR+TTEDPA NF PDTGRI +RS G G+RLDG +AFAGA I+PYYDSLLVK+ A
Sbjct: 343 YAIQCRITTEDPANNFMPDTGRITAYRSPGGFGVRLDGGNAFAGAEITPYYDSLLVKLTA 402
Query: 360 HAADLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDENPQLFTLQ 419
+ + A+M RALREFR+RGVKTNIPFL NVL + F G T FIDE P+LF
Sbjct: 403 WGRTFEQAVARMRRALREFRIRGVKTNIPFLENVLKHPDFRAGDYTTSFIDETPELFDFP 462
Query: 420 PTKNRAQKLLNYLGTVLVNGP------STPLATPLLPA-EVTPPVPE 459
++R KLL Y+ V VNG P LP +++ P P
Sbjct: 463 KRRDRGTKLLTYIADVTVNGFPGVKKKPPVFPDPRLPKVDLSAPPPA 509
Score = 464 bits (1196), Expect = e-145
Identities = 178/313 (56%), Positives = 224/313 (71%), Gaps = 4/313 (1%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAGLLKP AA L+ A++E+ D+PIH+HTHDTSG G+A+ +A AEAG D+VDVAV SM
Sbjct: 712 DMAGLLKPAAAYELVSALKEEV-DLPIHLHTHDTSGNGLATYLAAAEAGVDIVDVAVASM 770
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPFECTTTMKSGNADV 589
SG+TSQPS+ ++VA+L+G++ DTGLDL I S YWE R YAPFE + +KS +V
Sbjct: 771 SGLTSQPSLNSIVAALEGTERDTGLDLDAIRKLSPYWEAVRPYYAPFE--SGLKSPTTEV 828
Query: 590 YLNEIPGGQYTNLQFQAYSLGLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDFAQFM 649
YL+E+PGGQY+NL+ QA +LGLG+ FE+VK+ Y N + GDI+KVTPSSKVVGD A FM
Sbjct: 829 YLHEMPGGQYSNLKQQARALGLGDRFEEVKEMYAAVNRMFGDIVKVTPSSKVVGDMALFM 888
Query: 650 VQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDMPRIEGRPGAS 709
VQN LT E+V E+L FP SVV FL+G +G P GFPEPL+ KVLK I RPG
Sbjct: 889 VQNGLTPEDVYEPGEDLDFPDSVVSFLKGELGQPPGGFPEPLQKKVLKGEEPITVRPGEL 948
Query: 710 LPPFDFGKLKTELQERHP-EATDRDVMSAALYPQVTEDYLTFRESFGPVDKLDTRIFLTG 768
L P DF + EL+E+ E TDRDV+S LYP+V EDY+ RE +G V L T F G
Sbjct: 949 LEPVDFEAERAELEEKLGREVTDRDVLSYLLYPKVFEDYIKHREEYGDVSVLPTPTFFYG 1008
Query: 769 PKVGEEFEVKIQP 781
+ GEE EV+I+P
Sbjct: 1009 LRPGEEIEVEIEP 1021
Score = 243 bits (622), Expect = 4e-66
Identities = 84/136 (61%), Positives = 101/136 (74%), Gaps = 1/136 (0%)
Query: 769 PKVGEEFEVKIQPPQGFRQILKSKGPEAFAKAVRQNKSLLLMDTTFRDAHQSLLATRVRS 828
P++ + ++ PP G +QIL GPE FA +R K +LL DTTFRDAHQSLLATRVR+
Sbjct: 496 PRLPK-VDLSAPPPAGTKQILDELGPEGFADWLRDQKRVLLTDTTFRDAHQSLLATRVRT 554
Query: 829 HDLLKISPFVAHKFNNLYSLENWGGATFDVALRFLHECPWERLEEMRKQIPNIPFQMLLR 888
DLL+I+P A NL+SLE WGGATFDVA RFL E PWERL E+R+ PN+ FQMLLR
Sbjct: 555 KDLLRIAPATARLLPNLFSLEMWGGATFDVAYRFLKEDPWERLAELREAAPNVLFQMLLR 614
Query: 889 GANAVGYTNYPDNEMH 904
G+NAVGYTNYPDN +
Sbjct: 615 GSNAVGYTNYPDNVVR 630
Score = 174 bits (445), Expect = 2e-44
Identities = 59/101 (58%), Positives = 76/101 (75%)
Query: 969 MLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAAGKAGGVV 1028
MLLRG+NAVGYTNYPDNVV F + G+DVFR+FDSLN++ N+ + ++A + G +
Sbjct: 611 MLLRGSNAVGYTNYPDNVVRAFVREAAAAGIDVFRIFDSLNWVENMRVAIDAVRETGKIA 670
Query: 1029 EAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK 1069
EAAI YTGD+ DP++ KYDL YY +LA EL KAG H+L IK
Sbjct: 671 EAAICYTGDILDPARAKYDLDYYVDLAKELEKAGAHILAIK 711
Score = 92.5 bits (231), Expect = 6e-19
Identities = 32/60 (53%), Positives = 39/60 (65%)
Query: 906 HPKAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
KA PG VGAPMPGSV+ + VK GD+V+ G L V+ AMKME + APV G VK +
Sbjct: 1068 REKADPGNPGHVGAPMPGSVVTVLVKEGDEVKAGDPLAVIEAMKMETTITAPVDGTVKRV 1127
>gnl|CDD|130302 TIGR01235, pyruv_carbox, pyruvate carboxylase. This enzyme plays a
role in gluconeogensis but not glycolysis [Energy
metabolism, Glycolysis/gluconeogenesis].
Length = 1143
Score = 789 bits (2040), Expect = 0.0
Identities = 303/467 (64%), Positives = 358/467 (76%), Gaps = 6/467 (1%)
Query: 1 MHMHRQKADESYLVGKG--LPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQA 58
+ +HRQKADESY VG+G L P+EAYL+I EIIRVAK N VDAIHPGYGFLSE S+FA A
Sbjct: 35 LSLHRQKADESYQVGEGPDLGPIEAYLSIDEIIRVAKLNGVDAIHPGYGFLSENSEFADA 94
Query: 59 VLDAGIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLP 118
AGI FIGP V+ Q+GDKVAAR AI +GVP+VPGT GP T EE ++F G P
Sbjct: 95 CNKAGIIFIGPKAEVMDQLGDKVAARNLAIKAGVPVVPGTDGPPETMEEVLDFAAAIGYP 154
Query: 119 VIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLL 178
VI KA++GGGGRGMRVVR DV + FQRA SEAKAAFGN +++EK IERPRHIEVQLL
Sbjct: 155 VIIKASWGGGGRGMRVVRSEADVADAFQRAKSEAKAAFGNDEVYVEKLIERPRHIEVQLL 214
Query: 179 GDKAGNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTV 238
GDK GNVVHL+ERDCSVQRRHQKVVE+APAP+L VR+++ + AVKLAK V Y NAGTV
Sbjct: 215 GDKHGNVVHLFERDCSVQRRHQKVVEVAPAPYLSREVRDEIAEYAVKLAKAVNYINAGTV 274
Query: 239 EFLCDESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLP--ELGL-TQEKI 295
EFL D G+FYFIEVN R+QVEHTVTEEITG+D+VQ+QI +A+G +LP +LG+ QE I
Sbjct: 275 EFLVDNDGKFYFIEVNPRIQVEHTVTEEITGIDIVQAQIHIADGASLPTPQLGVPNQEDI 334
Query: 296 SPQGFAIQCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLV 355
G+AIQCRVTTEDPA NFQPDTGRIE +RS G GIRLDG +++AGAII+PYYDSLLV
Sbjct: 335 RTNGYAIQCRVTTEDPANNFQPDTGRIEAYRSAGGFGIRLDGGNSYAGAIITPYYDSLLV 394
Query: 356 KVIAHAADLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDENPQL 415
KV A A+ + + AKM+RALREFR+RGVKTNIPFL NVL + KF++G+ DT FID P+L
Sbjct: 395 KVSAWASTPEEAAAKMDRALREFRIRGVKTNIPFLENVLGHPKFLDGSYDTRFIDTTPEL 454
Query: 416 FTLQPTKNRAQKLLNYLGTVLVNGPSTPLATPLLPAEVTPPVPEIPL 462
F +++RA KLL YL V VNG L P E P V +
Sbjct: 455 FQFVKSQDRATKLLTYLADVTVNG-HPEAKDKLKPLENAPRVVVLYA 500
Score = 520 bits (1342), Expect = e-166
Identities = 190/312 (60%), Positives = 231/312 (74%), Gaps = 4/312 (1%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAGLLKP AAKLLI A+REK D+PIH HTHDTSG VASM+A EAG DVVDVAVDSM
Sbjct: 710 DMAGLLKPAAAKLLIKALREKT-DLPIHFHTHDTSGIAVASMLAAVEAGVDVVDVAVDSM 768
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPFECTTTMKSGNADV 589
SG+TSQPS+GA+VA+L+GS+ D GL++ I SAYWE R LYA FE +K ++V
Sbjct: 769 SGLTSQPSLGAIVAALEGSERDPGLNVAWIRELSAYWEAVRNLYAAFESD--LKGPASEV 826
Query: 590 YLNEIPGGQYTNLQFQAYSLGLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDFAQFM 649
YL+E+PGGQYTNLQFQA SLGLG+ + +VK+AYREAN + GDI+KVTPSSKVVGD A FM
Sbjct: 827 YLHEMPGGQYTNLQFQARSLGLGDRWHEVKQAYREANQMFGDIVKVTPSSKVVGDMALFM 886
Query: 650 VQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDMPRIEGRPGAS 709
V N LT ++V+ AEELSFP SVVEFL+G IG P+ GFPEPL+ KVLK I RPG+
Sbjct: 887 VSNDLTVDDVVEPAEELSFPDSVVEFLKGDIGQPHGGFPEPLQKKVLKGEKPITVRPGSL 946
Query: 710 LPPFDFGKLKTELQERH-PEATDRDVMSAALYPQVTEDYLTFRESFGPVDKLDTRIFLTG 768
L P D ++ +LQE+H E +D DV S A+YP+V D+ R+++GPV L T F G
Sbjct: 947 LEPADLDAIRKDLQEKHEREVSDFDVASYAMYPKVFTDFAKARDTYGPVSVLPTPAFFYG 1006
Query: 769 PKVGEEFEVKIQ 780
GEE EV I+
Sbjct: 1007 LADGEEIEVDIE 1018
Score = 240 bits (614), Expect = 3e-65
Identities = 90/130 (69%), Positives = 103/130 (79%)
Query: 782 PQGFRQILKSKGPEAFAKAVRQNKSLLLMDTTFRDAHQSLLATRVRSHDLLKISPFVAHK 841
P+G +QIL KGPE FA+ VR K +LL DTTFRDAHQSLLATRVR+HDL KI+P +H
Sbjct: 506 PRGTKQILDEKGPEGFAEWVRNQKRVLLTDTTFRDAHQSLLATRVRTHDLAKIAPTTSHA 565
Query: 842 FNNLYSLENWGGATFDVALRFLHECPWERLEEMRKQIPNIPFQMLLRGANAVGYTNYPDN 901
NL+SLE WGGATFDVA+RFLHE PWERLE++RK +PNI FQMLLRGAN VGYTNYPDN
Sbjct: 566 LPNLFSLECWGGATFDVAMRFLHEDPWERLEDLRKGVPNILFQMLLRGANGVGYTNYPDN 625
Query: 902 EMHIHPKAAK 911
+ K A
Sbjct: 626 VVKYFVKQAA 635
Score = 186 bits (473), Expect = 6e-48
Identities = 67/101 (66%), Positives = 80/101 (79%)
Query: 969 MLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAAGKAGGVV 1028
MLLRGAN VGYTNYPDNVV F + Q G+D+FRVFDSLN++ N+ +GM+A +AG VV
Sbjct: 609 MLLRGANGVGYTNYPDNVVKYFVKQAAQGGIDIFRVFDSLNWVENMRVGMDAVAEAGKVV 668
Query: 1029 EAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK 1069
EAAI YTGD+ DP++ KYDLKYY NLA EL KAG H+L IK
Sbjct: 669 EAAICYTGDILDPARPKYDLKYYTNLAVELEKAGAHILGIK 709
Score = 94.1 bits (234), Expect = 2e-19
Identities = 31/67 (46%), Positives = 39/67 (58%)
Query: 902 EMHIHPKAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGV 961
E + KA P VGAPMPG ++E++V G V KG LVVL AMKME +QAP G
Sbjct: 1062 EAAVRRKADPGNPAHVGAPMPGVIIEVKVSSGQAVNKGDPLVVLEAMKMETAIQAPKDGT 1121
Query: 962 VKSIDAS 968
+K +
Sbjct: 1122 IKEVLVK 1128
>gnl|CDD|223968 COG1038, PycA, Pyruvate carboxylase [Energy production and
conversion].
Length = 1149
Score = 737 bits (1904), Expect = 0.0
Identities = 284/467 (60%), Positives = 349/467 (74%), Gaps = 4/467 (0%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
+HR KADESYL+G+G PVEAYL+I EIIR+AK + DAIHPGYGFLSE +FA+A +A
Sbjct: 45 LHRFKADESYLIGEGKGPVEAYLSIDEIIRIAKRSGADAIHPGYGFLSENPEFARACAEA 104
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFK 122
GI FIGP P V+ +GDKV AR AAI +GVP++PGT GPI T EEA+EF +YG PV+ K
Sbjct: 105 GITFIGPKPEVLDMLGDKVKARNAAIKAGVPVIPGTDGPIETIEEALEFAEEYGYPVMIK 164
Query: 123 AAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKA 182
AA GGGGRGMRVVR D+ E F+RA SEAKAAFGN +++EK +E P+HIEVQ+LGD
Sbjct: 165 AAAGGGGRGMRVVRSEADLAEAFERAKSEAKAAFGNDEVYVEKLVENPKHIEVQILGDTH 224
Query: 183 GNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLC 242
GNVVHL+ERDCSVQRRHQKVVE+APAP+L +R+++ D AVKLA+++GY NAGTVEFL
Sbjct: 225 GNVVHLFERDCSVQRRHQKVVEVAPAPYLSPELRDEICDDAVKLARNIGYINAGTVEFLV 284
Query: 243 DESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTL--PELGLTQEK-ISPQG 299
DE G+FYFIEVN R+QVEHT+TEEITG+D+V++QI +A G TL PELGL Q+K I G
Sbjct: 285 DEDGKFYFIEVNPRIQVEHTITEEITGIDIVKAQIHIAAGATLHTPELGLPQQKDIRTHG 344
Query: 300 FAIQCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIA 359
+AIQCR+TTEDP F PDTGRI +RS G G+RLDG +A+AGA+I+PYYDSLLVKV
Sbjct: 345 YAIQCRITTEDPENGFIPDTGRITAYRSAGGFGVRLDGGNAYAGAVITPYYDSLLVKVTC 404
Query: 360 HAADLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDENPQLFTLQ 419
+ + + KM RALREFR+RGVKTNIPFL VL + F +G T FID P+LF
Sbjct: 405 WGSTFEEAIRKMIRALREFRIRGVKTNIPFLEAVLNHPDFRSGRYTTSFIDTTPELFQFP 464
Query: 420 PTKNRAQKLLNYLGTVLVNGPSTPLATPLLPAEVTPPVPEIPLGKLI 466
+++R KLL YL V VNG + P PA +P I + K
Sbjct: 465 KSQDRGTKLLTYLADVTVNGFPGLKSRP-KPAYDDAKLPVINVSKPP 510
Score = 453 bits (1167), Expect = e-141
Identities = 178/322 (55%), Positives = 227/322 (70%), Gaps = 6/322 (1%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAGLLKP AA LI A+RE D+PIH+HTHDTSG GVA+ +A EAG D+VDVA+ SM
Sbjct: 715 DMAGLLKPAAAYRLISALRETV-DLPIHLHTHDTSGNGVATYLAAVEAGVDIVDVAMASM 773
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPFECTTTMKSGNADV 589
SG+TSQPS+ ++VA+L G++ DTGLD++ + S YWE R+LYAPFE + +K +V
Sbjct: 774 SGLTSQPSLNSIVAALAGTERDTGLDIEAVRELSFYWEAVRKLYAPFE--SGLKGPATEV 831
Query: 590 YLNEIPGGQYTNLQFQAYSLGLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDFAQFM 649
YL+E+PGGQ TNL+ QA SLGLG+ +E+VK+AYRE N + GDI+KVTPSSKVVGD A FM
Sbjct: 832 YLHEMPGGQLTNLKQQARSLGLGDRWEEVKEAYREVNRMFGDIVKVTPSSKVVGDLALFM 891
Query: 650 VQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDMPRIEGRPGAS 709
VQN LT E+V A +L FP SVV F +G +G P GFPEPL+ KVLK + RPG
Sbjct: 892 VQNDLTEEDVENDANDLDFPDSVVSFFRGELGQPPGGFPEPLQKKVLKGREPLTDRPGEL 951
Query: 710 LPPFDFGKLKTELQERH-PEATDRDVMSAALYPQVTEDYLTFRESFGPVDKLDTRIFLTG 768
L P DF ++ EL+E+ E +D+DV S LYP+V EDY RE++G V L T F G
Sbjct: 952 LEPADFEAIRKELEEKLGREVSDQDVASYLLYPKVFEDYQKHRETYGDVSVLPTPTFFYG 1011
Query: 769 PKVGEEFEVKIQPPQGFRQILK 790
+ GEE EV+I +G I+K
Sbjct: 1012 LRPGEEIEVEI--EKGKTLIIK 1031
Score = 230 bits (589), Expect = 4e-62
Identities = 84/126 (66%), Positives = 98/126 (77%)
Query: 776 EVKIQPPQGFRQILKSKGPEAFAKAVRQNKSLLLMDTTFRDAHQSLLATRVRSHDLLKIS 835
V PP+G +QIL GPE FA+ VR+ K++LL DTTFRDAHQSLLATRVR+HDL +I+
Sbjct: 505 NVSKPPPRGTKQILDELGPEGFARWVREQKAVLLTDTTFRDAHQSLLATRVRTHDLARIA 564
Query: 836 PFVAHKFNNLYSLENWGGATFDVALRFLHECPWERLEEMRKQIPNIPFQMLLRGANAVGY 895
P A L+SLE WGGATFDVA+RFL E PWERLE +RK +PN+ FQMLLRGAN VGY
Sbjct: 565 PATARALPQLFSLEMWGGATFDVAMRFLKEDPWERLERLRKAVPNVLFQMLLRGANGVGY 624
Query: 896 TNYPDN 901
NYPDN
Sbjct: 625 KNYPDN 630
Score = 169 bits (429), Expect = 1e-42
Identities = 57/101 (56%), Positives = 73/101 (72%)
Query: 969 MLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAAGKAGGVV 1028
MLLRGAN VGY NYPDNV+ +F + + G+DVFR+FDSLN++ + + ++A +AG V
Sbjct: 614 MLLRGANGVGYKNYPDNVIREFVKQAAKSGIDVFRIFDSLNWVEQMRVAIDAVREAGKVA 673
Query: 1029 EAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK 1069
EA I YTGD+ DP +KKY L YY LA EL KAG H+L IK
Sbjct: 674 EATICYTGDILDPGRKKYTLDYYVKLAKELEKAGAHILAIK 714
Score = 89.3 bits (222), Expect = 7e-18
Identities = 32/59 (54%), Positives = 40/59 (67%)
Query: 907 PKAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
KA PG +GAPMPG V+E++VK GDKV+KG L V+ AMKME + AP G VK +
Sbjct: 1072 RKADPGNPGHIGAPMPGVVVEVKVKKGDKVKKGDVLAVIEAMKMETTISAPFDGTVKEV 1130
>gnl|CDD|236307 PRK08591, PRK08591, acetyl-CoA carboxylase biotin carboxylase
subunit; Validated.
Length = 451
Score = 580 bits (1499), Expect = 0.0
Identities = 205/410 (50%), Positives = 277/410 (67%), Gaps = 5/410 (1%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
+H Q ADE+ +G P ++YLNIP II A+ DAIHPGYGFLSE +DFA+ D+
Sbjct: 40 LHVQLADEAVCIGPA-PSKKSYLNIPAIISAAEITGADAIHPGYGFLSENADFAEICEDS 98
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFK 122
G FIGPS ++ MGDKV A+ +GVP+VPG+ GP+ EEA+ + G PVI K
Sbjct: 99 GFTFIGPSAETIRLMGDKVTAKATMKKAGVPVVPGSDGPVDDEEEALAIAKEIGYPVIIK 158
Query: 123 AAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKA 182
A GGGGRGMRVVR ++E+ F A +EAKAAFGN +++EK++E PRHIE+Q+L D
Sbjct: 159 ATAGGGGRGMRVVRTEAELEKAFSMARAEAKAAFGNPGVYMEKYLENPRHIEIQVLADGH 218
Query: 183 GNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLC 242
GN +HL ERDCS+QRRHQKV+E AP+P + +R K+ + AVK AK +GY AGT+EFL
Sbjct: 219 GNAIHLGERDCSLQRRHQKVLEEAPSPAITEELRRKIGEAAVKAAKAIGYRGAGTIEFLY 278
Query: 243 DESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAI 302
+++G+FYFIE+N R+QVEH VTE ITGVDLV+ QIR+A G L + QE I +G AI
Sbjct: 279 EKNGEFYFIEMNTRIQVEHPVTEMITGVDLVKEQIRIAAGE---PLSIKQEDIVFRGHAI 335
Query: 303 QCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAA 362
+CR+ EDPAKNF P G+I + G G+R+D A + G I PYYDS++ K+I H
Sbjct: 336 ECRINAEDPAKNFMPSPGKITRYHPPGGPGVRVDSA-VYTGYTIPPYYDSMIGKLIVHGE 394
Query: 363 DLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDEN 412
+ + A+M RAL EF + G+KT IP L +L + F G + +++++
Sbjct: 395 TREEAIARMKRALSEFVIDGIKTTIPLHLRLLNDPNFQAGDYNIHYLEKK 444
>gnl|CDD|227111 COG4770, COG4770, Acetyl/propionyl-CoA carboxylase, alpha subunit
[Lipid metabolism].
Length = 645
Score = 551 bits (1421), Expect = 0.0
Identities = 213/424 (50%), Positives = 278/424 (65%), Gaps = 6/424 (1%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
+H + ADE+ +G P E+YL+I +II A+ AIHPGYGFLSE +DFAQAV DA
Sbjct: 40 LHVRMADEAVHIG-PAPAAESYLDIDKIIDAARRTGAQAIHPGYGFLSENADFAQAVEDA 98
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFK 122
G+ FIGPS ++ MGDK+AA++ A ++GVP VPG GPI E + + G PV+ K
Sbjct: 99 GLVFIGPSAGAIRAMGDKIAAKKLAAEAGVPTVPGYHGPIQDAAELVAIAEEIGYPVLIK 158
Query: 123 AAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKA 182
A+ GGGG+GMRVV E+ E + A EAKA+FG+ +FIEK++++PRHIE+Q+ D+
Sbjct: 159 ASAGGGGKGMRVVETPEEFAEALESARREAKASFGDDRVFIEKYLDKPRHIEIQVFADQH 218
Query: 183 GNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLC 242
GNVVHL ERDCS+QRRHQKV+E APAP L R M + AV AK VGY AGTVEF+
Sbjct: 219 GNVVHLGERDCSLQRRHQKVIEEAPAPFLTEETREAMGEAAVAAAKAVGYVGAGTVEFIV 278
Query: 243 DESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAI 302
D G FYF+E+N RLQVEH VTE ITG+DLV+ QIRVA G LP TQ+ I G AI
Sbjct: 279 DADGNFYFLEMNTRLQVEHPVTELITGIDLVEWQIRVASGEKLP---FTQDDIPLNGHAI 335
Query: 303 QCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAA 362
+ R+ EDPA+ F P TGR+ +R G G+R+D + G ISP+YD ++ K+I H A
Sbjct: 336 EARIYAEDPARGFLPSTGRLTRYRPPAGPGVRVD-SGVREGDEISPFYDPMIAKLIVHGA 394
Query: 363 DLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDEN-PQLFTLQPT 421
D + + ++ RAL EF V G+ TNIPFL ++ + +F G +DT FI LF P
Sbjct: 395 DREEALDRLRRALAEFEVEGIATNIPFLRALMADPRFRGGDLDTGFIAREIEDLFAPAPA 454
Query: 422 KNRA 425
A
Sbjct: 455 SADA 458
Score = 73.9 bits (182), Expect = 2e-13
Identities = 28/61 (45%), Positives = 39/61 (63%)
Query: 908 KAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSIDA 967
K A + G++ APMPG+V+ + VK G +V G LVVL AMKME ++AP GVV +
Sbjct: 569 KVAAASSGELLAPMPGTVVSVAVKEGQEVSAGDLLVVLEAMKMENTLRAPRDGVVAKLAV 628
Query: 968 S 968
+
Sbjct: 629 A 629
>gnl|CDD|236325 PRK08654, PRK08654, pyruvate carboxylase subunit A; Validated.
Length = 499
Score = 519 bits (1338), Expect = e-174
Identities = 200/413 (48%), Positives = 280/413 (67%), Gaps = 6/413 (1%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
+ + ADE+Y +G PP ++YLNI II VAK+ DAIHPGYGFL+E +FA+A A
Sbjct: 40 LFVKYADEAYPIGPA-PPSKSYLNIERIIDVAKKAGADAIHPGYGFLAENPEFAKACEKA 98
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFK 122
GI FIGPS V++ MG K+ A++ +GVP++PGT I EEA E + G PVI K
Sbjct: 99 GIVFIGPSSDVIEAMGSKINAKKLMKKAGVPVLPGTEEGIEDIEEAKEIAEEIGYPVIIK 158
Query: 123 AAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKA 182
A+ GGGG GMRVV E++E+ + S A++AFG+ +FIEK++E+PRHIE+Q+L DK
Sbjct: 159 ASAGGGGIGMRVVYSEEELEDAIESTQSIAQSAFGDSTVFIEKYLEKPRHIEIQILADKH 218
Query: 183 GNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLC 242
GNV+HL +R+CS+QRRHQK++E AP+P + +R +M + AVK AK + Y NAGTVEFL
Sbjct: 219 GNVIHLGDRECSIQRRHQKLIEEAPSPIMTPELRERMGEAAVKAAKAINYENAGTVEFLY 278
Query: 243 DESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAI 302
+G FYF+E+N RLQVEH +TE +TG+D+V+ QI++A G L QE I+ +G AI
Sbjct: 279 S-NGNFYFLEMNTRLQVEHPITEMVTGIDIVKEQIKIAAGEELS---FKQEDITIRGHAI 334
Query: 303 QCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAA 362
+CR+ EDP +F P G+I+ +RS G G+R+D + G I PYYDS++ K+I
Sbjct: 335 ECRINAEDPLNDFAPSPGKIKRYRSPGGPGVRVD-SGVHMGYEIPPYYDSMISKLIVWGR 393
Query: 363 DLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDENPQL 415
+ + A+M RAL E+ + GVKTNIPF V+ N+ FV G + T+FI+E +
Sbjct: 394 TREEAIARMRRALYEYVIVGVKTNIPFHKAVMENENFVRGNLHTHFIEEETTI 446
>gnl|CDD|223516 COG0439, AccC, Biotin carboxylase [Lipid metabolism].
Length = 449
Score = 514 bits (1325), Expect = e-173
Identities = 211/415 (50%), Positives = 279/415 (67%), Gaps = 5/415 (1%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
+H ADE+ +G P ++YLNI II A+E DAIHPGYGFLSE + FA+A +A
Sbjct: 40 LHVALADEAVCIG-PAPSADSYLNIDAIIAAAEETGADAIHPGYGFLSENAAFAEACAEA 98
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFK 122
G+ FIGPS +++MGDK+ AR+ +GVP+VPG+ G + EEA+ + G PVI K
Sbjct: 99 GLTFIGPSAEAIRRMGDKITARRLMAKAGVPVVPGSDGAVADNEEALAIAEEIGYPVIVK 158
Query: 123 AAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKA 182
AA GGGGRGMRVVR E++E F+ A EA+AAFGN +++EKFIE PRHIEVQ+LGD
Sbjct: 159 AAAGGGGRGMRVVRNEEELEAAFEAARGEAEAAFGNPRVYLEKFIEGPRHIEVQVLGDGH 218
Query: 183 GNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLC 242
GNV+HL ERDCS+QRRHQKV+E AP+P L +R K+ + AV+ AK +GY AGTVEFL
Sbjct: 219 GNVIHLGERDCSIQRRHQKVIEEAPSPLLTEELREKIGEAAVRAAKLIGYRGAGTVEFLY 278
Query: 243 DESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAI 302
D +G+FYFIE+N RLQVEH VTE +TG+DLV+ QIR+A G L L QE I +G AI
Sbjct: 279 DSNGEFYFIEMNTRLQVEHPVTEMVTGIDLVKEQIRIAAGE---PLSLKQEDIKFRGHAI 335
Query: 303 QCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAA 362
+CR+ EDP NF P G+I + G G+R+D G + PYYDS++ KVI H
Sbjct: 336 ECRINAEDPLGNFLPSPGKITRYAPPGGPGVRVDSGVY-DGYRVPPYYDSMIGKVIVHGR 394
Query: 363 DLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDENPQLFT 417
+ A+M RAL E + G+KTNIP L +L + F+ G +DT+F++ + +
Sbjct: 395 TRDEAIARMRRALDELVIDGIKTNIPLLQEILRDPDFLAGDLDTHFLETHLEPLA 449
>gnl|CDD|180406 PRK06111, PRK06111, acetyl-CoA carboxylase biotin carboxylase
subunit; Validated.
Length = 450
Score = 504 bits (1301), Expect = e-169
Identities = 193/406 (47%), Positives = 264/406 (65%), Gaps = 6/406 (1%)
Query: 4 HRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDAG 63
H + ADE+YL+G E+YLN+ +II +AK+ +AIHPGYG LSE + FA+ + G
Sbjct: 41 HVKMADEAYLIGGP-RVQESYLNLEKIIEIAKKTGAEAIHPGYGLLSENASFAERCKEEG 99
Query: 64 IRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKA 123
I FIGPS ++ +MG K+ AR+A +GVP+VPG + EEA+ + G PV+ KA
Sbjct: 100 IVFIGPSADIIAKMGSKIEARRAMQAAGVPVVPGITTNLEDAEEAIAIARQIGYPVMLKA 159
Query: 124 AYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAG 183
+ GGGG GM++V +++ + F+ A FGNG M+IEK+IE PRHIE+QLL D G
Sbjct: 160 SAGGGGIGMQLVETEQELTKAFESNKKRAANFFGNGEMYIEKYIEDPRHIEIQLLADTHG 219
Query: 184 NVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLCD 243
N V+L+ER+CSVQRRHQKV+E AP+P LD R M + AV+ AK +GY+NAGT+EFL D
Sbjct: 220 NTVYLWERECSVQRRHQKVIEEAPSPFLDEETRKAMGERAVQAAKAIGYTNAGTIEFLVD 279
Query: 244 ESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAIQ 303
E FYF+E+N RLQVEH VTEEITG+DLV+ Q+R+A G L TQ+ I G AI+
Sbjct: 280 EQKNFYFLEMNTRLQVEHPVTEEITGIDLVEQQLRIAAGEKLS---FTQDDIKRSGHAIE 336
Query: 304 CRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAAD 363
R+ EDP K F P G+I G G+R D A G ++P+YD ++ K+IAH
Sbjct: 337 VRIYAEDP-KTFFPSPGKITDLTLPGGEGVRHDHAVE-NGVTVTPFYDPMIAKLIAHGET 394
Query: 364 LQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFI 409
+ + ++++ AL E +V G+KTNIP LL VL + F G T F+
Sbjct: 395 REEAISRLHDALEELKVEGIKTNIPLLLQVLEDPVFKAGGYTTGFL 440
>gnl|CDD|129605 TIGR00514, accC, acetyl-CoA carboxylase, biotin carboxylase
subunit. This model represents the biotin carboxylase
subunit found usually as a component of acetyl-CoA
carboxylase. Acetyl-CoA carboxylase is designated EC
6.4.1.2 and this component, biotin carboxylase, has its
own designation, EC 6.3.4.14. Homologous domains are
found in eukaryotic forms of acetyl-CoA carboxylase and
in a number of other carboxylases (e.g. pyruvate
carboxylase), but seed members and trusted cutoff are
selected so as to exclude these. In some systems, the
biotin carboxyl carrier protein and this protein (biotin
carboxylase) may be shared by different
carboxyltransferases. However, this model is not
intended to identify the biotin carboxylase domain of
propionyl-coA carboxylase. The model should hit the full
length of proteins, except for chloroplast transit
peptides in plants. If it hits a domain only of a longer
protein, there may be a problem with the identification
[Fatty acid and phospholipid metabolism, Biosynthesis].
Length = 449
Score = 490 bits (1263), Expect = e-163
Identities = 195/409 (47%), Positives = 272/409 (66%), Gaps = 5/409 (1%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
+H ADE+ +G P ++YLNIP II A+ DAIHPGYGFLSE ++FA+ +
Sbjct: 40 LHVLLADEAVCIGPA-PSAKSYLNIPNIISAAEITGADAIHPGYGFLSENANFAEQCERS 98
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFK 122
G FIGPS ++ MGDKV+A + +GVP VPG+ G + EE + + G PVI K
Sbjct: 99 GFTFIGPSAESIRLMGDKVSAIETMKKAGVPCVPGSDGLVEDEEENVRIAKRIGYPVIIK 158
Query: 123 AAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKA 182
A GGGGRGMRVVR+ +++ ++ +EAKAAFGN ++IEK+IE PRH+E+Q+L DK
Sbjct: 159 ATAGGGGRGMRVVREPDELVKSISMTRAEAKAAFGNDGVYIEKYIENPRHVEIQVLADKY 218
Query: 183 GNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLC 242
GN ++L ERDCS+QRRHQK++E AP+P L +R KM D AVK A +GY AGTVEFL
Sbjct: 219 GNAIYLGERDCSIQRRHQKLLEEAPSPALTPELRRKMGDAAVKAAVSIGYRGAGTVEFLL 278
Query: 243 DESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAI 302
D++G+FYF+E+N R+QVEH VTE ITGVDL++ QIR+A G L L QE + +G AI
Sbjct: 279 DKNGEFYFMEMNTRIQVEHPVTEMITGVDLIKEQIRIAAGEPLS---LKQEDVVVRGHAI 335
Query: 303 QCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAA 362
+CR+ EDP K F P GRI + G G+R D ++G + PYYDS++ K+I +
Sbjct: 336 ECRINAEDPIKTFLPSPGRITRYLPPGGPGVRWDSH-VYSGYTVPPYYDSMIGKLITYGK 394
Query: 363 DLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDE 411
+ + A+M RAL EF + G+KT IPF +L ++ F +G + +++++
Sbjct: 395 TREVAIARMKRALSEFIIDGIKTTIPFHQRILEDENFQHGGTNIHYLEK 443
>gnl|CDD|180150 PRK05586, PRK05586, biotin carboxylase; Validated.
Length = 447
Score = 484 bits (1248), Expect = e-161
Identities = 202/410 (49%), Positives = 273/410 (66%), Gaps = 5/410 (1%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
+H Q ADE+ +G ++YLNI II AIHPG+GFLSE S FA+ +
Sbjct: 40 LHVQLADEAVCIGPASSK-DSYLNIQNIISATVLTGAQAIHPGFGFLSENSKFAKMCKEC 98
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFK 122
I FIGP ++ MG+K AR+ I +GVP+VPG+ G I EEA+E + G PV+ K
Sbjct: 99 NIVFIGPDSETIELMGNKSNAREIMIKAGVPVVPGSEGEIENEEEALEIAKEIGYPVMVK 158
Query: 123 AAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKA 182
A+ GGGGRG+R+VR E++ + F A SEAKAAFG+ +M+IEKFIE P+HIE Q+LGD
Sbjct: 159 ASAGGGGRGIRIVRSEEELIKAFNTAKSEAKAAFGDDSMYIEKFIENPKHIEFQILGDNY 218
Query: 183 GNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLC 242
GNVVHL ERDCS+QRR+QKV+E AP+P + +R KM ++AVK AK V Y NAGT+EFL
Sbjct: 219 GNVVHLGERDCSLQRRNQKVLEEAPSPVMTEELRKKMGEIAVKAAKAVNYKNAGTIEFLL 278
Query: 243 DESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAI 302
D+ G FYF+E+N R+QVEH +TE ITGVDLV+ QI++A G +L + QE I G +I
Sbjct: 279 DKDGNFYFMEMNTRIQVEHPITEMITGVDLVKEQIKIAYGE---KLSIKQEDIKINGHSI 335
Query: 303 QCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAA 362
+CR+ EDP F P G+IE G+G+R+D A ++G I PYYDS++ K+I +
Sbjct: 336 ECRINAEDPKNGFMPCPGKIEELYIPGGLGVRVDSA-VYSGYTIPPYYDSMIGKLIVYGK 394
Query: 363 DLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDEN 412
D + + KM RAL EF + GV TNI F +L +++F+ G DT FI++
Sbjct: 395 DREEAIQKMKRALGEFIIEGVNTNIDFQFIILEDEEFIKGTYDTSFIEKK 444
>gnl|CDD|180865 PRK07178, PRK07178, pyruvate carboxylase subunit A; Validated.
Length = 472
Score = 483 bits (1244), Expect = e-160
Identities = 198/413 (47%), Positives = 277/413 (67%), Gaps = 6/413 (1%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
+H ++ADE+Y +G P+ YLN ++ +A E DA+HPGYGFLSE ++ A+ +
Sbjct: 40 LHVKRADEAYSIGAD--PLAGYLNPRRLVNLAVETGCDALHPGYGFLSENAELAEICAER 97
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFK 122
GI+FIGPS V+++MGDK AR+A I +GVP+ PG+ G + +EA+ + G PV+ K
Sbjct: 98 GIKFIGPSAEVIRRMGDKTEARRAMIKAGVPVTPGSEGNLADLDEALAEAERIGYPVMLK 157
Query: 123 AAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKA 182
A GGGGRG+R E++E+NF R SEA AFG+ +F+EK I P+HIEVQ+L D
Sbjct: 158 ATSGGGGRGIRRCNSREELEQNFPRVISEATKAFGSAEVFLEKCIVNPKHIEVQILADSH 217
Query: 183 GNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLC 242
GNVVHL+ERDCS+QRR+QK++EIAP+P L R + DLAV+ AK VGY NAGTVEFL
Sbjct: 218 GNVVHLFERDCSIQRRNQKLIEIAPSPQLTPEQRAYIGDLAVRAAKAVGYENAGTVEFLL 277
Query: 243 DESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAI 302
D G+ YF+E+N R+QVEHT+TEEITG+D+V+ QIR+A G+ L QE I +GFA+
Sbjct: 278 DADGEVYFMEMNTRVQVEHTITEEITGIDIVREQIRIASGLPLS---YKQEDIQHRGFAL 334
Query: 303 QCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAA 362
Q R+ EDP +F P G+I + + G G+R D A + G I PYYDS+ K+I A
Sbjct: 335 QFRINAEDPKNDFLPSFGKITRYYAPGGPGVRTDTA-IYTGYTIPPYYDSMCAKLIVWAL 393
Query: 363 DLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDENPQL 415
+ + + RAL + RV+GVKT IP+ +L N +F +G +T F++ +P+L
Sbjct: 394 TWEEALDRGRRALDDMRVQGVKTTIPYYQEILRNPEFRSGQFNTSFVESHPEL 446
>gnl|CDD|169452 PRK08463, PRK08463, acetyl-CoA carboxylase subunit A; Validated.
Length = 478
Score = 456 bits (1176), Expect = e-150
Identities = 206/426 (48%), Positives = 279/426 (65%), Gaps = 8/426 (1%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
+H + ADE+Y +G P++ YL++ I+ +AK DAIHPGYGFLSE +FA+AV DA
Sbjct: 40 LHVKIADEAYRIGTD--PIKGYLDVKRIVEIAKACGADAIHPGYGFLSENYEFAKAVEDA 97
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGT-PGPITTTEEAMEFCLKYGLPVIF 121
GI FIGP V+++MG+K AR +G+PIVPGT + EE F K G PVI
Sbjct: 98 GIIFIGPKSEVIRKMGNKNIARYLMKKNGIPIVPGTEKLNSESMEEIKIFARKIGYPVIL 157
Query: 122 KAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDK 181
KA+ GGGGRG+RVV K ED+E F+ EA A F N +F+EK++ PRHIE Q+LGD
Sbjct: 158 KASGGGGGRGIRVVHKEEDLENAFESCKREALAYFNNDEVFMEKYVVNPRHIEFQILGDN 217
Query: 182 AGNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFL 241
GN++HL ERDCS+QRRHQKV+EIAP P + N+R M AV AK VGY+NAGT+EFL
Sbjct: 218 YGNIIHLCERDCSIQRRHQKVIEIAPCPSISDNLRKTMGVTAVAAAKAVGYTNAGTIEFL 277
Query: 242 CDESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFA 301
D+ +FYF+E+N R+QVEH VTEEITG+DL+ QIR+A G L L Q I P+GFA
Sbjct: 278 LDDYNRFYFMEMNTRIQVEHGVTEEITGIDLIVRQIRIAAGEILD---LEQSDIKPRGFA 334
Query: 302 IQCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHA 361
I+ R+T E+ KNF P G+I + G +R+D + + I PYYDS+L K+I A
Sbjct: 335 IEARITAENVWKNFIPSPGKITEYYPALGPSVRVD-SHIYKDYTIPPYYDSMLAKLIVKA 393
Query: 362 ADLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDENPQLFTLQPT 421
+ K+ RAL+EF + G++T IPFL+ + ++F G DT +I+ + Q L+ T
Sbjct: 394 TSYDLAVNKLERALKEFVIDGIRTTIPFLIAITKTREFRRGYFDTSYIETHMQEL-LEKT 452
Query: 422 KNRAQK 427
++R Q+
Sbjct: 453 EDRHQE 458
>gnl|CDD|236269 PRK08462, PRK08462, biotin carboxylase; Validated.
Length = 445
Score = 450 bits (1160), Expect = e-148
Identities = 198/405 (48%), Positives = 271/405 (66%), Gaps = 7/405 (1%)
Query: 8 ADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDAGIRFI 67
AD +G G E+YLNIP II A+ + DAI PGYGFLSE +F + I+FI
Sbjct: 47 ADAKICIG-GAKSSESYLNIPAIISAAEIFEADAIFPGYGFLSENQNFVEICSHHNIKFI 105
Query: 68 GPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGG 127
GPS V+ M DK A++ +GVP++PG+ G + + EEA + + G PVI KAA GG
Sbjct: 106 GPSVEVMALMSDKSKAKEVMKRAGVPVIPGSDGALKSYEEAKKIAKEIGYPVILKAAAGG 165
Query: 128 GGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVVH 187
GGRGMRVV D+E + A SEA +AFG+G M++EKFI PRHIEVQ+LGDK GNV+H
Sbjct: 166 GGRGMRVVEDESDLENLYLAAESEALSAFGDGTMYMEKFINNPRHIEVQILGDKHGNVIH 225
Query: 188 LYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLCDESGQ 247
+ ERDCS+QRRHQK++E +PA LD R ++ + A+K AK +GY AGT EFL D +
Sbjct: 226 VGERDCSLQRRHQKLIEESPAVVLDEKTRERLHETAIKAAKAIGYEGAGTFEFLLDSNLD 285
Query: 248 FYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAIQCRVT 307
FYF+E+N RLQVEHTV+E ++G+DL++ I++AEG LP QE I +G AI+CR+T
Sbjct: 286 FYFMEMNTRLQVEHTVSEMVSGLDLIEWMIKIAEGEELPS----QESIKLKGHAIECRIT 341
Query: 308 TEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAADLQSS 367
EDP K F P G+I + + G +R+D + A+AG ++ PYYDS++ K+I D +
Sbjct: 342 AEDP-KKFYPSPGKITKWIAPGGRNVRMD-SHAYAGYVVPPYYDSMIGKLIVWGEDRNRA 399
Query: 368 CAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFIDEN 412
AKM RAL+EF+V G+KT IPF L ++ N F+N DT +++E+
Sbjct: 400 IAKMKRALKEFKVEGIKTTIPFHLEMMENADFINNKYDTKYLEEH 444
>gnl|CDD|183781 PRK12833, PRK12833, acetyl-CoA carboxylase biotin carboxylase
subunit; Provisional.
Length = 467
Score = 431 bits (1111), Expect = e-141
Identities = 184/407 (45%), Positives = 259/407 (63%), Gaps = 13/407 (3%)
Query: 8 ADESYLVGKGLPPVEA---YLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDAGI 64
ADE+ +G P A YLN I+ A++ DAIHPGYGFLSE + FA+AV AG+
Sbjct: 48 ADEAVHIG----PSHAAKSYLNPAAILAAARQCGADAIHPGYGFLSENAAFAEAVEAAGL 103
Query: 65 RFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAA 124
F+GP ++ MGDK AR+ A +GVP VPG+ G + + + A+E + G P++ KAA
Sbjct: 104 IFVGPDAQTIRTMGDKARARRTARRAGVPTVPGSDGVVASLDAALEVAARIGYPLMIKAA 163
Query: 125 YGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGN 184
GGGGRG+RV + A EA+AAFG+G +++E+FI R RHIEVQ+LGD
Sbjct: 164 AGGGGRGIRVAHDAAQLAAELPLAQREAQAAFGDGGVYLERFIARARHIEVQILGD-GER 222
Query: 185 VVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLCD- 243
VVHL+ER+CS+QRR QK++E AP+P L R+ + AV+LA+ VGY AGT+E+L D
Sbjct: 223 VVHLFERECSLQRRRQKILEEAPSPSLTPAQRDALCASAVRLARQVGYRGAGTLEYLFDD 282
Query: 244 ESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAIQ 303
G+FYFIE+N R+QVEH VTE ITG+DLVQ +R+A+G L Q I+ +G A++
Sbjct: 283 ARGEFYFIEMNTRIQVEHPVTEAITGIDLVQEMLRIADG---EPLRFAQGDIALRGAALE 339
Query: 304 CRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAAD 363
CR+ EDP ++F P+ GRI+ +G G+R+D + + G + P+YDSLL K+I H D
Sbjct: 340 CRINAEDPLRDFFPNPGRIDALVWPQGPGVRVD-SLLYPGYRVPPFYDSLLAKLIVHGED 398
Query: 364 LQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFID 410
++ A+ RALRE R+ G+KT P +L + G T F++
Sbjct: 399 RAAALARAARALRELRIDGMKTTAPLHRALLADADVRAGRFHTNFLE 445
>gnl|CDD|233980 TIGR02712, urea_carbox, urea carboxylase. Members of this family
are ATP-dependent urea carboxylase, including
characterized members from Oleomonas sagaranensis (alpha
class Proteobacterium) and yeasts such as Saccharomyces
cerevisiae. The allophanate hydrolase domain of the
yeast enzyme is not included in this model and is
represented by an adjacent gene in Oleomonas
sagaranensis. The fusion of urea carboxylase and
allophanate hydrolase is designated urea amidolyase. The
enzyme from Oleomonas sagaranensis was shown to be
highly active on acetamide and formamide as well as urea
[Central intermediary metabolism, Nitrogen metabolism].
Length = 1201
Score = 424 bits (1092), Expect = e-130
Identities = 176/410 (42%), Positives = 259/410 (63%), Gaps = 11/410 (2%)
Query: 4 HRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDAG 63
H ADE+ +G G P E+YL+I +I+ AK+ AIHPGYGFLSE + FA+A AG
Sbjct: 40 HVLDADEAVCLG-GAPAAESYLDIDKILAAAKKTGAQAIHPGYGFLSENAAFAEACEAAG 98
Query: 64 IRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKA 123
I F+GP+P +++ G K AR+ A +GVP++PGT G +++ +EA+E + G PV+ K+
Sbjct: 99 IVFVGPTPEQIRKFGLKHTARELAEAAGVPLLPGT-GLLSSLDEALEAAKEIGYPVMLKS 157
Query: 124 AYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAG 183
GGGG GM+ ++ E F+ ++ FG+ +F+E+F+E RH+EVQ+ GD G
Sbjct: 158 TAGGGGIGMQKCDSAAELAEAFETVKRLGESFFGDAGVFLERFVENARHVEVQIFGDGKG 217
Query: 184 NVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLCD 243
VV L ERDCS+QRR+QKVVE PAP+L R + A +L + V Y +AGTVEF+ D
Sbjct: 218 KVVALGERDCSLQRRNQKVVEETPAPNLPPETRQALLAAAERLGEAVNYRSAGTVEFIYD 277
Query: 244 ES-GQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAI 302
E+ +FYF+EVN RLQVEH VTE +TG+DLV+ IR+A G L ++P+G AI
Sbjct: 278 EARDEFYFLEVNTRLQVEHPVTEMVTGLDLVEWMIRIAAGELPDFASLNIS-LTPRGAAI 336
Query: 303 QCRVTTEDPAKNFQPDTGRIE--VFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAH 360
+ RV E+PAKNFQP G + F +R+D G +SP YD +L K+I H
Sbjct: 337 EARVYAENPAKNFQPSPGLLTDVQFPD----DVRVDTWVE-TGTEVSPEYDPMLAKIIVH 391
Query: 361 AADLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFID 410
+D + + K+++AL E RV G++TN+ +L ++L+++ F + V T ++
Sbjct: 392 GSDREDAILKLHQALAETRVYGIETNLDYLRSILSSETFRSAQVSTRTLN 441
Score = 63.1 bits (154), Expect = 7e-10
Identities = 26/50 (52%), Positives = 33/50 (66%)
Query: 916 QVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
QV + G+ ++ V+VGD+VE G LV+L AMKMEM V APV G V I
Sbjct: 1134 QVESEYAGNFWKVLVEVGDRVEAGQPLVILEAMKMEMPVSAPVAGKVTKI 1183
Score = 31.9 bits (73), Expect = 2.4
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 916 QVGAPMPGSVMEIRVKVGDKVEKGAALVVL 945
V AP+ G V +I + GD V+ G + VL
Sbjct: 1171 PVSAPVAGKVTKILCQPGDMVDAGDIVAVL 1200
>gnl|CDD|190425 pfam02786, CPSase_L_D2, Carbamoyl-phosphate synthase L chain, ATP
binding domain. Carbamoyl-phosphate synthase catalyzes
the ATP-dependent synthesis of carbamyl-phosphate from
glutamine or ammonia and bicarbonate. This important
enzyme initiates both the urea cycle and the
biosynthesis of arginine and/or pyrimidines. The
carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes
is a heterodimer of a small and large chain. The small
chain promotes the hydrolysis of glutamine to ammonia,
which is used by the large chain to synthesise carbamoyl
phosphate. See pfam00988. The small chain has a GATase
domain in the carboxyl terminus. See pfam00117. The ATP
binding domain (this one) has an ATP-grasp fold.
Length = 211
Score = 280 bits (719), Expect = 9e-88
Identities = 104/211 (49%), Positives = 140/211 (66%), Gaps = 1/211 (0%)
Query: 79 DKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKM 138
DKV + A ++GVP VPGT GP+ T EEA+ + G PVI KAA+GGGG GM + R
Sbjct: 1 DKVLFKAAMKEAGVPTVPGTAGPVETEEEALAAAKEIGYPVIIKAAFGGGGLGMGIARNE 60
Query: 139 EDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVVHLYERDCSVQRR 198
E++ E F A +EA AAFGN + +EK ++ P+HIE Q+L D GN + + R+CS QRR
Sbjct: 61 EELAELFALALAEAPAAFGNPQVLVEKSLKGPKHIEYQVLRDAHGNCITVCNRECSDQRR 120
Query: 199 HQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLCD-ESGQFYFIEVNARL 257
QK +E+AP+ L R + + AVK+A+H+GY AGTVEF D SG++YFIE+N RL
Sbjct: 121 TQKSIEVAPSQTLTDEERQMLREAAVKIARHLGYVGAGTVEFALDPFSGEYYFIEMNTRL 180
Query: 258 QVEHTVTEEITGVDLVQSQIRVAEGMTLPEL 288
QVEH + E+ TG DL + ++A G LPEL
Sbjct: 181 QVEHALAEKATGYDLAKEAAKIALGYPLPEL 211
>gnl|CDD|217032 pfam02436, PYC_OADA, Conserved carboxylase domain. This domain
represents a conserved region in pyruvate carboxylase
(PYC), oxaloacetate decarboxylase alpha chain (OADA),
and transcarboxylase 5s subunit. The domain is found
adjacent to the HMGL-like domain (pfam00682) and often
close to the biotin_lipoyl domain (pfam00364) of biotin
requiring enzymes.
Length = 198
Score = 272 bits (699), Expect = 5e-85
Identities = 89/194 (45%), Positives = 120/194 (61%), Gaps = 4/194 (2%)
Query: 589 VYLNEIPGGQYTNLQFQAYSLGLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDFAQF 648
VYL++IPGGQ +NL+ Q GLG+ +E+V + Y LGDI VTPSS++VGD A F
Sbjct: 1 VYLHQIPGGQLSNLKSQLKEQGLGDRWEEVLEEYPRVRKDLGDIPLVTPSSQIVGDQAVF 60
Query: 649 MVQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDMPRIEGRPGA 708
V N LT + FPKSVV++L+G G P GFPE L+ KVLK I RP
Sbjct: 61 NVLNGLT---PVGEGRYKDFPKSVVDYLKGEYGQPPGGFPEELQKKVLKGEEPITCRPAD 117
Query: 709 SLPPFDFGKLKTELQERH-PEATDRDVMSAALYPQVTEDYLTFRESFGPVDKLDTRIFLT 767
L P D KL+ EL+E+ + +D DV+S AL+P+V E +L RE +G V L T +F
Sbjct: 118 LLEPVDLEKLRAELEEKAGRKLSDEDVLSYALFPKVAEKFLEHREEYGDVSVLPTPVFFY 177
Query: 768 GPKVGEEFEVKIQP 781
G +VGEE+ V+++P
Sbjct: 178 GMEVGEEYSVEVEP 191
>gnl|CDD|163675 cd07937, DRE_TIM_PC_TC_5S, Pyruvate carboxylase and
Transcarboxylase 5S, carboxyltransferase domain. This
family includes the carboxyltransferase domains of
pyruvate carboxylase (PC) and the transcarboxylase (TC)
5S subunit. Transcarboxylase 5S is a cobalt-dependent
metalloenzyme subunit of the biotin-dependent
transcarboxylase multienzyme complex. Transcarboxylase
5S transfers carbon dioxide from the 1.3S biotin to
pyruvate in the second of two carboxylation reactions
catalyzed by TC. The first reaction involves the
transfer of carbon dioxide from methylmalonyl-CoA to the
1.3S biotin, and is catalyzed by the 12S subunit. These
two steps allow a carboxylate group to be transferred
from oxaloacetate to propionyl-CoA to yield pyruvate and
methylmalonyl-CoA. The catalytic domain of
transcarboxylase 5S has a canonical TIM-barrel fold with
a large C-terminal extension that forms a funnel leading
to the active site. Transcarboxylase 5S forms a
homodimer and there are six dimers per complex. In
addition to the catalytic domain, transcarboxylase 5S
has several other domains including a
carbamoyl-phosphate synthase domain, a biotin
carboxylase domain, a carboxyltransferase domain, and an
ATP-grasp domain. Pyruvate carboxylase, like TC, is a
biotin-dependent enzyme that catalyzes the carboxylation
of pyruvate to produce oxaloacetate. In mammals, PC has
critical roles in gluconeogenesis, lipogenesis,
glyceroneogenesis, and insulin secretion. Inherited PC
deficiencies are linked to serious diseases in humans
such as lactic acidemia, hypoglycemia, psychomotor
retardation, and death. PC is a single-chain enzyme and
is active only in its homotetrameric form. PC has three
domains, an N-terminal biotin carboxylase domain, a
carboxyltransferase domain (this alignment model), and a
C-terminal biotin-carboxyl carrier protein domain. This
family belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 275
Score = 190 bits (485), Expect = 2e-54
Identities = 62/106 (58%), Positives = 78/106 (73%), Gaps = 5/106 (4%)
Query: 809 LMDTTFRDAHQSLLATRVRSHDLLKISPFVAHKFNNLYSLENWGGATFDVALRFLHECPW 868
+ DTT RDAHQSLLATR+R+ D+L I+ + +SLE WGGATFDV +RFL+E PW
Sbjct: 1 ITDTTLRDAHQSLLATRMRTEDMLPIAEALDE--AGFFSLEVWGGATFDVCMRFLNEDPW 58
Query: 869 ERLEEMRKQIPNIPFQMLLRGANAVGYTNYPDN--EMHIHPKAAKS 912
ERL E+RK +PN P QMLLRG N VGY +YPD+ E+ + KAAK+
Sbjct: 59 ERLRELRKAMPNTPLQMLLRGQNLVGYRHYPDDVVELFVE-KAAKN 103
Score = 179 bits (456), Expect = 2e-50
Identities = 57/107 (53%), Positives = 79/107 (73%), Gaps = 1/107 (0%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAGLL P AA L+ A++++ +PIH+HTHDTSG VA+ +A AEAG D+VD A+ +
Sbjct: 170 DMAGLLTPYAAYELVKALKKEVG-LPIHLHTHDTSGLAVATYLAAAEAGVDIVDTAISPL 228
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPF 576
SG TSQPS ++VA+L+G+ DTGLDL+ + S Y+E+ R+ YAPF
Sbjct: 229 SGGTSQPSTESMVAALRGTGRDTGLDLEKLEEISEYFEEVRKKYAPF 275
Score = 166 bits (422), Expect = 7e-46
Identities = 47/109 (43%), Positives = 65/109 (59%), Gaps = 6/109 (5%)
Query: 961 VVKSIDASMLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEA 1020
+ + MLLRG N VGY +YPD+VV F + + + G+D+FR+FD+LN + NL + ++A
Sbjct: 67 AMPNTPLQMLLRGQNLVGYRHYPDDVVELFVEKAAKNGIDIFRIFDALNDVRNLEVAIKA 126
Query: 1021 AGKAGGVVEAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK 1069
KAG VE AI YTG + L+YY LA EL G +CIK
Sbjct: 127 VKKAGKHVEGAICYTGS------PVHTLEYYVKLAKELEDMGADSICIK 169
>gnl|CDD|214878 smart00878, Biotin_carb_C, Biotin carboxylase C-terminal domain.
Biotin carboxylase is a component of the acetyl-CoA
carboxylase multi-component enzyme which catalyses the
first committed step in fatty acid synthesis in animals,
plants and bacteria. Most of the active site residues
reported in reference are in this C-terminal domain.
Length = 107
Score = 164 bits (419), Expect = 1e-47
Identities = 49/108 (45%), Positives = 68/108 (62%), Gaps = 1/108 (0%)
Query: 303 QCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAA 362
+CR+ EDPA F P GRI +R G G+R+D + G + PYYDS++ K+I
Sbjct: 1 ECRINAEDPANGFLPSPGRITRYRFPGGPGVRVDSG-VYEGYEVPPYYDSMIAKLIVWGE 59
Query: 363 DLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFID 410
D + + A++ RAL EFR+RGVKTNIPFL +L + F G VDT F++
Sbjct: 60 DREEAIARLRRALDEFRIRGVKTNIPFLRALLRHPDFRAGDVDTGFLE 107
>gnl|CDD|236449 PRK09282, PRK09282, pyruvate carboxylase subunit B; Validated.
Length = 592
Score = 178 bits (454), Expect = 4e-47
Identities = 105/334 (31%), Positives = 168/334 (50%), Gaps = 47/334 (14%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAGLL P AA L+ A++E+ D+P+ +H+H TSG + + EAG D++D A+ +
Sbjct: 175 DMAGLLTPYAAYELVKALKEEV-DLPVQLHSHCTSGLAPMTYLKAVEAGVDIIDTAISPL 233
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPFECTTTMKSGNADV 589
+ TSQP ++VA+L+G+ DTGLDL+ + + Y+ + R+ Y FE T+ + V
Sbjct: 234 AFGTSQPPTESMVAALKGTPYDTGLDLELLFEIAEYFREVRKKYKQFESEFTI--VDTRV 291
Query: 590 YLNEIPGGQYTNLQFQAYSLG----LGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDF 645
++++PGG +NL Q L E E++ + + LG VTP+S++VG
Sbjct: 292 LIHQVPGGMISNLVSQLKEQNALDKLDEVLEEIPRVRED----LGYPPLVTPTSQIVGTQ 347
Query: 646 AQFMVQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEP----LRSKVLKDMPR 701
A V N LT E R + K V ++++G G P P P LR K++ D
Sbjct: 348 A---VLNVLTGE----RYK--VITKEVKDYVKGLYGRP----PAPINEELRKKIIGDEEP 394
Query: 702 IEGRPGASLPPFDFGKLKTELQE---RHPEATDRDVMSAALYPQVTEDYLTFRESFGPVD 758
I RP L P + K + E +E E DV++ AL+PQ+ + +L RE+
Sbjct: 395 ITCRPADLLEP-ELEKARKEAEELGKSEKE----DVLTYALFPQIAKKFLEEREAGELKP 449
Query: 759 KLDTRIFLTGPKV-----------GEEFEVKIQP 781
+ + + GE++EVKI+
Sbjct: 450 EPEPKEAAAAGAEGIPTEFKVEVDGEKYEVKIEG 483
Score = 144 bits (366), Expect = 7e-36
Identities = 56/92 (60%), Positives = 70/92 (76%), Gaps = 6/92 (6%)
Query: 811 DTTFRDAHQSLLATRVRSHDLLKISPFVAHKFNNL--YSLENWGGATFDVALRFLHECPW 868
DTT RDAHQSLLATR+R+ D+L I A K + + +SLE WGGATFDV +R+L+E PW
Sbjct: 8 DTTLRDAHQSLLATRMRTEDMLPI----AEKLDKVGFWSLEVWGGATFDVCIRYLNEDPW 63
Query: 869 ERLEEMRKQIPNIPFQMLLRGANAVGYTNYPD 900
ERL +++K +PN P QMLLRG N VGY +YPD
Sbjct: 64 ERLRKLKKALPNTPLQMLLRGQNLVGYRHYPD 95
Score = 109 bits (275), Expect = 1e-24
Identities = 45/101 (44%), Positives = 65/101 (64%), Gaps = 6/101 (5%)
Query: 969 MLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAAGKAGGVV 1028
MLLRG N VGY +YPD+VV KF + + + G+D+FR+FD+LN + N+ + ++AA KAG V
Sbjct: 80 MLLRGQNLVGYRHYPDDVVEKFVEKAAENGIDIFRIFDALNDVRNMEVAIKAAKKAGAHV 139
Query: 1029 EAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK 1069
+ ISYT S + ++ Y LA EL + G +CIK
Sbjct: 140 QGTISYT--TS----PVHTIEKYVELAKELEEMGCDSICIK 174
Score = 78.3 bits (194), Expect = 9e-15
Identities = 33/67 (49%), Positives = 46/67 (68%)
Query: 899 PDNEMHIHPKAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPV 958
P E+ + + S PG V +PMPG+V++++VK GDKV+ G ++VL AMKME +QAPV
Sbjct: 507 PLKEIVVGGRPRASAPGAVTSPMPGTVVKVKVKEGDKVKAGDTVLVLEAMKMENEIQAPV 566
Query: 959 QGVVKSI 965
G VK I
Sbjct: 567 DGTVKEI 573
>gnl|CDD|227349 COG5016, COG5016, Pyruvate/oxaloacetate carboxyltransferase [Energy
production and conversion].
Length = 472
Score = 167 bits (424), Expect = 4e-44
Identities = 97/284 (34%), Positives = 148/284 (52%), Gaps = 13/284 (4%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAGLL P A L+ AI+++ P +P+ +HTH TSG + + EAG D +D A+ +
Sbjct: 177 DMAGLLTPYEAYELVKAIKKELP-VPVELHTHATSGMAEMTYLKAVEAGVDGIDTAISPL 235
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPFECTTTMKSGNADV 589
SG TSQP+ +VA+L+G+ DTGLDL+ + + Y+ + R+ Y K + +
Sbjct: 236 SGGTSQPATETMVAALRGTGYDTGLDLELLEEIAEYFREVRKKYK-GLLEPQAKGVDPRI 294
Query: 590 YLNEIPGGQYTNLQFQAYSLGLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDFAQFM 649
+ ++PGG +NL+ Q + E+V + LG VTP+S++VG A
Sbjct: 295 LIYQVPGGMLSNLESQLKEQNALDKLEEVLEEVPRVREDLGYPPLVTPTSQIVGTQA--- 351
Query: 650 VQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDM-PRIEGRPGA 708
V N LT E R + + K ++++G G L K+L D I RP
Sbjct: 352 VLNVLTGE----RYKVI--TKETKDYVKGLYGRTPAPINAELIEKILGDEEKPITCRPAD 405
Query: 709 SLPPFDFGKLKTELQERHPEATDRDVMSAALYPQVTEDYLTFRE 752
L P + KLK EL+E E + DV++ AL+PQV + +L RE
Sbjct: 406 LLEP-ELDKLKKELEELAIEEEEEDVLTYALFPQVAKKFLEGRE 448
Score = 137 bits (347), Expect = 3e-34
Identities = 53/100 (53%), Positives = 67/100 (67%), Gaps = 6/100 (6%)
Query: 803 QNKSLLLMDTTFRDAHQSLLATRVRSHDLLKISPFVAHKFNNL--YSLENWGGATFDVAL 860
K + + DT RD HQSLLATR+R+ D+L I A + + +SLE WGGATFD +
Sbjct: 2 AMKKIKITDTVLRDGHQSLLATRMRTEDMLPI----AEALDKVGYWSLEVWGGATFDACI 57
Query: 861 RFLHECPWERLEEMRKQIPNIPFQMLLRGANAVGYTNYPD 900
RFL+E PWERL E++K +PN QMLLRG N VGY +Y D
Sbjct: 58 RFLNEDPWERLRELKKAVPNTKLQMLLRGQNLVGYRHYAD 97
Score = 102 bits (255), Expect = 2e-22
Identities = 47/101 (46%), Positives = 65/101 (64%), Gaps = 6/101 (5%)
Query: 969 MLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAAGKAGGVV 1028
MLLRG N VGY +Y D+VV KF + + + G+DVFR+FD+LN + NL ++AA K G V
Sbjct: 82 MLLRGQNLVGYRHYADDVVEKFVEKAAENGIDVFRIFDALNDVRNLKTAIKAAKKHGAHV 141
Query: 1029 EAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK 1069
+ ISYT + P + L+YY LA EL++ G +CIK
Sbjct: 142 QGTISYT---TSPV---HTLEYYVELAKELLEMGVDSICIK 176
>gnl|CDD|202395 pfam02785, Biotin_carb_C, Biotin carboxylase C-terminal domain.
Biotin carboxylase is a component of the acetyl-CoA
carboxylase multi-component enzyme which catalyzes the
first committed step in fatty acid synthesis in animals,
plants and bacteria. Most of the active site residues
reported in reference are in this C-terminal domain.
Length = 107
Score = 149 bits (378), Expect = 3e-42
Identities = 47/108 (43%), Positives = 67/108 (62%), Gaps = 1/108 (0%)
Query: 303 QCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASAFAGAIISPYYDSLLVKVIAHAA 362
+ R+ EDPA F P G+I +R G G+R+D + G +SPYYDS++ K+I H
Sbjct: 1 EARIYAEDPANGFLPSPGKITRYRFPGGPGVRVDSG-VYEGDEVSPYYDSMIAKLIVHGP 59
Query: 363 DLQSSCAKMNRALREFRVRGVKTNIPFLLNVLTNQKFVNGAVDTYFID 410
D + + A++ RAL E R+ GVKTNIPFL +L + F G VDT F++
Sbjct: 60 DREEAIARLRRALAETRIEGVKTNIPFLRAILEHPDFRAGEVDTGFLE 107
>gnl|CDD|183446 PRK12331, PRK12331, oxaloacetate decarboxylase; Provisional.
Length = 448
Score = 152 bits (386), Expect = 2e-39
Identities = 93/287 (32%), Positives = 145/287 (50%), Gaps = 18/287 (6%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASM--IACAEAGADVVDVAVD 527
DMAG+L P A L+ I+E +P+ +HTH TS G+A M + EAGAD++D A+
Sbjct: 175 DMAGILTPYVAYELVKRIKEA-VTVPLEVHTHATS--GIAEMTYLKAIEAGADIIDTAIS 231
Query: 528 SMSGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLY-APFECTTTMKSGN 586
+G TSQP+ ++VA+LQ DTGLDL+++S + Y+ R Y +K
Sbjct: 232 PFAGGTSQPATESMVAALQDLGYDTGLDLEELSEIAEYFNPIRDHYREEGILNPKVKDVE 291
Query: 587 ADVYLNEIPGGQYTNLQFQAYSLGLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDFA 646
+ ++PGG +NL Q G + +E+V K + LG VTP S++VG A
Sbjct: 292 PKTLIYQVPGGMLSNLLSQLKEQGAEDKYEEVLKEVPKVRADLGYPPLVTPLSQMVGTQA 351
Query: 647 QFMVQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDMPRIEGRP 706
+ N ++ E P + ++++G G P E ++ K++ D I RP
Sbjct: 352 ---LMNVISGERYKM------VPNEIKDYVRGLYGRPPAPIAEEIKKKIIGDEEVITCRP 402
Query: 707 GASLPPFDFGKLKTELQERHPEATDRDVMSAALYPQVTEDYLTFRES 753
+ P KL+ E+ E + DV+S AL+PQ +D+L RE
Sbjct: 403 ADLIEP-QLEKLREEIAEYAES--EEDVLSYALFPQQAKDFLGRRED 446
Score = 122 bits (307), Expect = 3e-29
Identities = 47/95 (49%), Positives = 62/95 (65%), Gaps = 6/95 (6%)
Query: 809 LMDTTFRDAHQSLLATRVRSHDLLKISPFVAHKFNNL--YSLENWGGATFDVALRFLHEC 866
+ +T RD QSL+ATR+ + ++L I K +N +SLE WGGATFD LRFL+E
Sbjct: 6 ITETVLRDGQQSLIATRMTTEEMLPI----LEKLDNAGYHSLEMWGGATFDACLRFLNED 61
Query: 867 PWERLEEMRKQIPNIPFQMLLRGANAVGYTNYPDN 901
PWERL ++RK + QMLLRG N +GY NY D+
Sbjct: 62 PWERLRKIRKAVKKTKLQMLLRGQNLLGYRNYADD 96
Score = 92.8 bits (231), Expect = 1e-19
Identities = 46/109 (42%), Positives = 63/109 (57%), Gaps = 6/109 (5%)
Query: 961 VVKSIDASMLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEA 1020
VK MLLRG N +GY NY D+VV F SV+ G+D+ R+FD+LN + NL ++A
Sbjct: 72 AVKKTKLQMLLRGQNLLGYRNYADDVVESFVQKSVENGIDIIRIFDALNDVRNLETAVKA 131
Query: 1021 AGKAGGVVEAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK 1069
KAGG + AISYT S + + Y+ LA E+ + G +CIK
Sbjct: 132 TKKAGGHAQVAISYT--TSP----VHTIDYFVKLAKEMQEMGADSICIK 174
>gnl|CDD|233273 TIGR01108, oadA, oxaloacetate decarboxylase alpha subunit. This
model describes the bacterial oxaloacetate decarboxylase
alpha subunit and its equivalents in archaea. The
oxaloacetate decarboxylase Na+ pump is the paradigm of
the family of Na+ transport decarboxylases that present
in bacteria and archaea. It a multi subunit enzyme
consisting of a peripheral alpha-subunit and integral
membrane subunits beta and gamma. The energy released by
the decarboxylation reaction of oxaloacetate is coupled
to Na+ ion pumping across the membrane [Transport and
binding proteins, Cations and iron carrying compounds,
Energy metabolism, Other].
Length = 582
Score = 154 bits (390), Expect = 4e-39
Identities = 95/285 (33%), Positives = 158/285 (55%), Gaps = 15/285 (5%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAG+L P+AA L+ A++++ +P+H+H+H T+G +++ EAGAD +D A+ SM
Sbjct: 170 DMAGILTPKAAYELVSALKKRF-GLPVHLHSHATTGMAEMALLKAIEAGADGIDTAISSM 228
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPFECTTTMKSGNADV 589
SG TS P +VA+L+G+ DTGLD++ + +AY+ + R+ Y+ FE +K ++ +
Sbjct: 229 SGGTSHPPTETMVAALRGTGYDTGLDIELLLEIAAYFREVRKKYSQFE--GQLKGPDSRI 286
Query: 590 YLNEIPGGQYTNLQFQAYSLGLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDFAQFM 649
+ ++PGG +NL+ Q + ++V + LG VTP+S++VG A
Sbjct: 287 LVAQVPGGMLSNLESQLKEQNALDKLDEVLEEIPRVREDLGYPPLVTPTSQIVGTQA--- 343
Query: 650 VQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDM-PRIEGRPGA 708
V N LT E R + ++ K +L+G G L+ K+L D P ++ RP
Sbjct: 344 VLNVLTGE----RYKTIT--KETKGYLKGEYGRTPAPINAELQRKILGDEKPIVDCRPAD 397
Query: 709 SLPPFDFGKLKTELQERHPEA-TDRDVMSAALYPQVTEDYLTFRE 752
L P + KL+ E++E E + DV++ AL+PQV +L R
Sbjct: 398 LLEP-ELDKLRAEVREAGAEKNSIEDVLTYALFPQVGLKFLENRH 441
Score = 128 bits (323), Expect = 1e-30
Identities = 52/93 (55%), Positives = 65/93 (69%), Gaps = 6/93 (6%)
Query: 811 DTTFRDAHQSLLATRVRSHDLLKISPFVAHKFN--NLYSLENWGGATFDVALRFLHECPW 868
D RDAHQSL ATR+R+ D+L I A K + +SLE WGGATFD +RFL+E PW
Sbjct: 3 DVVLRDAHQSLFATRMRTEDMLPI----AEKLDDVGYWSLEVWGGATFDACIRFLNEDPW 58
Query: 869 ERLEEMRKQIPNIPFQMLLRGANAVGYTNYPDN 901
ERL E++K +PN P QMLLRG N +GY +Y D+
Sbjct: 59 ERLRELKKALPNTPLQMLLRGQNLLGYRHYADD 91
Score = 94.9 bits (236), Expect = 6e-20
Identities = 47/110 (42%), Positives = 69/110 (62%), Gaps = 7/110 (6%)
Query: 968 SMLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAAGKAGGV 1027
MLLRG N +GY +Y D+VV +F +V+ GMDVFR+FD+LN NL ++AA K G
Sbjct: 74 QMLLRGQNLLGYRHYADDVVERFVKKAVENGMDVFRIFDALNDPRNLQAAIQAAKKHGAH 133
Query: 1028 VEAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK-VRILLSP 1076
+ ISYT + P + L+ Y +LA+EL++ G +CIK + +L+P
Sbjct: 134 AQGTISYT---TSPV---HTLETYLDLAEELLEMGVDSICIKDMAGILTP 177
Score = 54.4 bits (131), Expect = 3e-07
Identities = 23/67 (34%), Positives = 35/67 (52%)
Query: 899 PDNEMHIHPKAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPV 958
P N A V AP+ GS+++++V G V +G L++L AMKME ++A
Sbjct: 502 PANTSGGTVAAKAGAGTPVTAPIAGSIVKVKVSEGQTVAEGEVLLILEAMKMETEIKAAA 561
Query: 959 QGVVKSI 965
G V+ I
Sbjct: 562 AGTVREI 568
>gnl|CDD|237592 PRK14040, PRK14040, oxaloacetate decarboxylase; Provisional.
Length = 593
Score = 138 bits (351), Expect = 4e-34
Identities = 101/301 (33%), Positives = 157/301 (52%), Gaps = 29/301 (9%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAGLLKP AA L+ I+++ D+P+H+H H T+G A+++ EAG D VD A+ SM
Sbjct: 176 DMAGLLKPYAAYELVSRIKKRV-DVPLHLHCHATTGLSTATLLKAIEAGIDGVDTAISSM 234
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPFECTTTMKSGNADV 589
S + +VA+L+G++ DTGLD+ + +AY+ + R+ YA FE +K ++ +
Sbjct: 235 SMTYGHSATETLVATLEGTERDTGLDILKLEEIAAYFREVRKKYAKFE--GQLKGVDSRI 292
Query: 590 YLNEIPGGQYTNLQFQAYSLGLGEFFEDVKK---AYREANLLLGDIIKVTPSSKVVGDFA 646
+ ++PGG TN++ Q G + ++V RE LG I VTP+S++VG A
Sbjct: 293 LVAQVPGGMLTNMESQLKEQGAADKLDEVLAEIPRVRED---LGFIPLVTPTSQIVGTQA 349
Query: 647 QFMVQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDMPRIEGRP 706
V N LT E R + ++ K L+G G L+++VL+ I RP
Sbjct: 350 ---VLNVLTGE----RYKTIT--KETAGVLKGEYGATPAPVNAELQARVLEGAEPITCRP 400
Query: 707 GASLPPFDFGKLKTELQE-------RHPEATDRDVMSAALYPQVTEDYLTFR---ESFGP 756
L P + KL+ EL+ E DV++ AL+PQ+ +L R +F P
Sbjct: 401 ADLLAP-ELDKLEAELRRQAQEKGITLAENAIDDVLTYALFPQIGLKFLENRHNPAAFEP 459
Query: 757 V 757
V
Sbjct: 460 V 460
Score = 124 bits (314), Expect = 2e-29
Identities = 54/100 (54%), Positives = 68/100 (68%), Gaps = 6/100 (6%)
Query: 803 QNKSLLLMDTTFRDAHQSLLATRVRSHDLLKISPFVAHKFNNL--YSLENWGGATFDVAL 860
+K L + D RDAHQSL ATR+R D+L I A K + + +SLE+WGGATFD +
Sbjct: 1 MSKPLAITDVVLRDAHQSLFATRLRLDDMLPI----AAKLDKVGYWSLESWGGATFDACI 56
Query: 861 RFLHECPWERLEEMRKQIPNIPFQMLLRGANAVGYTNYPD 900
RFL E PWERL E++K +PN P QMLLRG N +GY +Y D
Sbjct: 57 RFLGEDPWERLRELKKAMPNTPQQMLLRGQNLLGYRHYAD 96
Score = 81.9 bits (203), Expect = 6e-16
Identities = 42/101 (41%), Positives = 60/101 (59%), Gaps = 6/101 (5%)
Query: 969 MLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAAGKAGGVV 1028
MLLRG N +GY +Y D+VV +F + +V+ GMDVFRVFD++N NL ++A K G
Sbjct: 81 MLLRGQNLLGYRHYADDVVERFVERAVKNGMDVFRVFDAMNDPRNLETALKAVRKVGAHA 140
Query: 1029 EAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK 1069
+ +SYT S + L+ + +LA +L G LCIK
Sbjct: 141 QGTLSYT--TSP----VHTLQTWVDLAKQLEDMGVDSLCIK 175
Score = 58.0 bits (141), Expect = 2e-08
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 907 PKAAKSVPGQ-VGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
A + G+ V AP+ G++ ++ V G V +G L++L AMKME ++A G V+ I
Sbjct: 516 AAAPAAAAGEPVTAPLAGNIFKVIVTEGQTVAEGDVLLILEAMKMETEIRAAQAGTVRGI 575
Query: 966 D 966
Sbjct: 576 A 576
>gnl|CDD|237593 PRK14041, PRK14041, oxaloacetate decarboxylase; Provisional.
Length = 467
Score = 132 bits (334), Expect = 1e-32
Identities = 85/283 (30%), Positives = 145/283 (51%), Gaps = 23/283 (8%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAGLL P+ A L+ A+++K +P+ +H+H T+G + +A EAGAD+ D A+
Sbjct: 174 DMAGLLTPKRAYELVKALKKKF-GVPVEVHSHCTTGLASLAYLAAVEAGADMFDTAISPF 232
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPFECTTTMKSGNADV 589
S TSQP ++ + + + +T D K + Y+ + R+ Y+ ++ MKS ++ +
Sbjct: 233 SMGTSQPPFESMYYAFRENGKETDFDRKALKFLVEYFTKVREKYSEYD--VGMKSPDSRI 290
Query: 590 YLNEIPGGQYTNL--QFQAYSL--GLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDF 645
+++IPGG Y+NL Q + + L + E+V + ++ LG VTP+S++VG
Sbjct: 291 LVSQIPGGMYSNLVKQLKEQKMLHKLDKVLEEVPRVRKD----LGYPPLVTPTSQIVGVQ 346
Query: 646 AQFMVQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDMPRIEGR 705
A V N LT E R + ++ +++G G P E L K+L D I+ R
Sbjct: 347 A---VLNVLTGE----RYKRVT--NETKNYVKGLYGRPPAPIDEELMKKILGDEKPIDCR 397
Query: 706 PGASLPPFDFGKLKTELQERHPEATDRDVMSAALYPQVTEDYL 748
P L P + K + EL TD D++ + +V + +L
Sbjct: 398 PADLLEP-ELEKARKELGILAE--TDEDLLIYVILGEVGKKFL 437
Score = 122 bits (308), Expect = 3e-29
Identities = 52/94 (55%), Positives = 67/94 (71%), Gaps = 2/94 (2%)
Query: 808 LLMDTTFRDAHQSLLATRVRSHDLLKISPFVAHKFNNLYSLENWGGATFDVALRFLHECP 867
+ +DTT RD HQSL+ATR+R+ D+L A YS+E WGGATFDV +RFL+E P
Sbjct: 4 MFVDTTLRDGHQSLIATRMRTEDMLPA--LEAFDRMGFYSMEVWGGATFDVCVRFLNENP 61
Query: 868 WERLEEMRKQIPNIPFQMLLRGANAVGYTNYPDN 901
WERL+E+RK++ N QMLLRG N VGY +Y D+
Sbjct: 62 WERLKEIRKRLKNTKIQMLLRGQNLVGYRHYADD 95
Score = 97.2 bits (242), Expect = 6e-21
Identities = 50/116 (43%), Positives = 67/116 (57%), Gaps = 7/116 (6%)
Query: 962 VKSIDASMLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAA 1021
+K+ MLLRG N VGY +Y D+VV F + G+D+ R+FD+LN + NL +E A
Sbjct: 72 LKNTKIQMLLRGQNLVGYRHYADDVVELFVKKVAEYGLDIIRIFDALNDIRNLEKSIEVA 131
Query: 1022 GKAGGVVEAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK-VRILLSP 1076
K G V+ AISYT VS + L+YY A ELV G +CIK + LL+P
Sbjct: 132 KKHGAHVQGAISYT--VS----PVHTLEYYLEFARELVDMGVDSICIKDMAGLLTP 181
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 127 bits (321), Expect = 2e-32
Identities = 40/99 (40%), Positives = 59/99 (59%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
D GL P L+ A+RE PD+P+ +HTH+T G VA+ +A EAGAD VD +V+ +
Sbjct: 167 DTVGLATPEEVAELVKALREALPDVPLGLHTHNTLGLAVANSLAALEAGADRVDGSVNGL 226
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQ 568
+ +VA+L+G IDTG+DL+ + S Y E+
Sbjct: 227 GERAGNAATEDLVAALEGLGIDTGIDLEKLLEISRYVEE 265
Score = 71.7 bits (177), Expect = 1e-13
Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 810 MDTTFRDAHQSLLATRVRSHDLLKISPFVAHKFNNLYSLENWGGATFDVALRFLHECPWE 869
DTT RD QS AT + D L+I+ + + S+E GA+ E WE
Sbjct: 1 TDTTLRDGLQSEGATF-STEDKLEIAEALDE--AGVDSIEVGSGASPKAV--PQMEDDWE 55
Query: 870 RLEEMRKQIPNIPFQMLLRG 889
L +RK +PN+ Q L+R
Sbjct: 56 VLRAIRKLVPNVKLQALVRN 75
Score = 61.3 bits (150), Expect = 5e-10
Identities = 24/95 (25%), Positives = 40/95 (42%), Gaps = 20/95 (21%)
Query: 989 KFCDLSVQVGMDVFRVFDSLNY--------------LPNLILGMEAAGKAGGVVEAAISY 1034
K + +++ G+D R+FDS + L N +EAA +AG VE ++
Sbjct: 78 KGIERALEAGVDEVRIFDSASETHSRKNLNKSREEDLENAEEAIEAAKEAGLEVEGSLED 137
Query: 1035 TGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK 1069
K D +Y +A L +AG + +K
Sbjct: 138 AFGC------KTDPEYVLEVAKALEEAGADEISLK 166
>gnl|CDD|183445 PRK12330, PRK12330, oxaloacetate decarboxylase; Provisional.
Length = 499
Score = 123 bits (311), Expect = 1e-29
Identities = 89/296 (30%), Positives = 143/296 (48%), Gaps = 28/296 (9%)
Query: 470 DMAGLLKPRAAKLLIGAIREKH-PDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDS 528
DMA LLKP+ A ++ I+E D I++H H T+G + S++ EAG DVVD A+ S
Sbjct: 176 DMAALLKPQPAYDIVKGIKEACGEDTRINLHCHSTTGVTLVSLMKAIEAGVDVVDTAISS 235
Query: 529 MS-GMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPFECTTTMKSGNA 587
MS G P+ ++V L+G+ T LD+ + ++++ R Y FE TT
Sbjct: 236 MSLGPGHNPTE-SLVEMLEGTGYTTKLDMDRLLKIRDHFKKVRPKYKEFESKTT--GVET 292
Query: 588 DVYLNEIPGGQYTNLQFQAYSLGLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDFAQ 647
+++ ++IPGG +N++ Q G G+ ++V + G VTPSS++VG A
Sbjct: 293 EIFKSQIPGGMLSNMESQLKQQGAGDRMDEVLEEVPRVRKDAGYPPLVTPSSQIVGTQAV 352
Query: 648 FMVQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDMPR------ 701
F V ++ R + L+ EF +G Y P +V++ +
Sbjct: 353 FNV--------LMGRYKVLT-----GEFADLMLGY-YGETPGERNPEVVEQAKKQAKKEP 398
Query: 702 IEGRPGASLPPFDFGKLKTELQE-RHPEATDRDVMSAALYPQVTEDYLTFRESFGP 756
I RP L P ++ KL+ E + +D DV++ AL+PQV + R GP
Sbjct: 399 ITCRPADLLEP-EWDKLRAEALALEGCDGSDEDVLTYALFPQVAPKFFATRAE-GP 452
Score = 99.1 bits (247), Expect = 2e-21
Identities = 44/86 (51%), Positives = 57/86 (66%), Gaps = 2/86 (2%)
Query: 815 RDAHQSLLATRVRSHDLLKISPFVAHKFNNLYSLENWGGATFDVALRFLHECPWERLEEM 874
RDAHQSL+ATR+ D++ + + +S+E WGGATFD +RFL+E PWERL
Sbjct: 13 RDAHQSLMATRMAMEDMVGACEDIDNA--GYWSVECWGGATFDACIRFLNEDPWERLRTF 70
Query: 875 RKQIPNIPFQMLLRGANAVGYTNYPD 900
RK +PN QMLLRG N +GY +Y D
Sbjct: 71 RKLMPNSRLQMLLRGQNLLGYRHYED 96
Score = 86.7 bits (215), Expect = 2e-17
Identities = 45/109 (41%), Positives = 60/109 (55%), Gaps = 7/109 (6%)
Query: 969 MLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAAGKAGGVV 1028
MLLRG N +GY +Y D VV +F + S + GMDVFRVFD+LN NL M+A K G
Sbjct: 81 MLLRGQNLLGYRHYEDEVVDRFVEKSAENGMDVFRVFDALNDPRNLEHAMKAVKKVGKHA 140
Query: 1029 EAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK-VRILLSP 1076
+ I YT VS + ++ + A L+ G +CIK + LL P
Sbjct: 141 QGTICYT--VS----PIHTVEGFVEQAKRLLDMGADSICIKDMAALLKP 183
>gnl|CDD|172536 PRK14042, PRK14042, pyruvate carboxylase subunit B; Provisional.
Length = 596
Score = 114 bits (287), Expect = 3e-26
Identities = 88/284 (30%), Positives = 134/284 (47%), Gaps = 15/284 (5%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAGLL P L +++ +P+H+H+H TSG AG + +D A+ S
Sbjct: 175 DMAGLLTPTVTVELYAGLKQA-TGLPVHLHSHSTSGLASICHYEAVLAGCNHIDTAISSF 233
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAPFECTTTMKSGNADV 589
SG S P A+VA+L + DT LDL + Y++ R+ Y+ FE + ++ + V
Sbjct: 234 SGGASHPPTEALVAALTDTPYDTELDLNILLEIDDYFKAVRKKYSQFE--SEAQNIDPRV 291
Query: 590 YLNEIPGGQYTNLQFQAYSLGLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDFAQFM 649
L ++PGG +NL Q + + V K LG VTP+S+VVG A
Sbjct: 292 QLYQVPGGMISNLYNQLKEQNALDKMDAVHKEIPRVRKDLGYPPLVTPTSQVVGTQA--- 348
Query: 650 VQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDMPRIEGRPGAS 709
V N LT E E+ + QG GTP LR K + IE RPG
Sbjct: 349 VINVLTGERYKTITNEVKL------YCQGKYGTPPGKISSALRKKAIGRTEVIEVRPG-D 401
Query: 710 LPPFDFGKLKTELQERHPEATDRDVMSAALYPQVTEDYLTFRES 753
L P + +L+ E+ + +D DV+ A++P++ +L R++
Sbjct: 402 LLPNELDQLQNEISDL--ALSDEDVLLYAMFPEIGRQFLEQRKN 443
Score = 102 bits (254), Expect = 3e-22
Identities = 49/105 (46%), Positives = 68/105 (64%), Gaps = 6/105 (5%)
Query: 808 LLMDTTFRDAHQSLLATRVRSHDLLKISPFVAHKFNNL--YSLENWGGATFDVALRFLHE 865
+ D T RDAHQ L+ATR+R+ D+L I +K +++ +++E WGGATFD LRFL E
Sbjct: 5 FITDVTLRDAHQCLIATRMRTEDMLPI----CNKMDDVGFWAMEVWGGATFDACLRFLKE 60
Query: 866 CPWERLEEMRKQIPNIPFQMLLRGANAVGYTNYPDNEMHIHPKAA 910
PW RL ++R+ +PN MLLRG N +GY NY D+ + K A
Sbjct: 61 DPWSRLRQLRQALPNTQLSMLLRGQNLLGYRNYADDVVRAFVKLA 105
Score = 66.7 bits (162), Expect = 4e-11
Identities = 43/110 (39%), Positives = 60/110 (54%), Gaps = 7/110 (6%)
Query: 968 SMLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAAGKAGGV 1027
SMLLRG N +GY NY D+VV F L+V G+DVFRVFD+LN NL + ++A
Sbjct: 79 SMLLRGQNLLGYRNYADDVVRAFVKLAVNNGVDVFRVFDALNDARNLKVAIDAIKSHKKH 138
Query: 1028 VEAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK-VRILLSP 1076
+ AI YT + + L + L +L + G + IK + LL+P
Sbjct: 139 AQGAICYT------TSPVHTLDNFLELGKKLAEMGCDSIAIKDMAGLLTP 182
Score = 56.7 bits (136), Expect = 4e-08
Identities = 24/52 (46%), Positives = 35/52 (67%)
Query: 914 PGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
PG + +PGS++ I V GD+V+ G A++V+ AMKME ++AP GVV I
Sbjct: 525 PGDITVAIPGSIIAIHVSAGDEVKAGQAVLVIEAMKMETEIKAPANGVVAEI 576
>gnl|CDD|201133 pfam00289, CPSase_L_chain, Carbamoyl-phosphate synthase L chain,
N-terminal domain. Carbamoyl-phosphate synthase
catalyzes the ATP-dependent synthesis of
carbamyl-phosphate from glutamine or ammonia and
bicarbonate. This important enzyme initiates both the
urea cycle and the biosynthesis of arginine and/or
pyrimidines. The carbamoyl-phosphate synthase (CPS)
enzyme in prokaryotes is a heterodimer of a small and
large chain. The small chain promotes the hydrolysis of
glutamine to ammonia, which is used by the large chain
to synthesise carbamoyl phosphate. See pfam00988. The
small chain has a GATase domain in the carboxyl
terminus. See pfam00117.
Length = 108
Score = 103 bits (259), Expect = 4e-26
Identities = 39/70 (55%), Positives = 51/70 (72%), Gaps = 1/70 (1%)
Query: 2 HMHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLD 61
H + ADE+Y +G G P E+YLNI I+ +A++ DAIHPGYGFLSE ++FA+A +
Sbjct: 38 STHVRLADEAYFLGPG-PASESYLNIERILDIAEKEGADAIHPGYGFLSENAEFAEACEE 96
Query: 62 AGIRFIGPSP 71
AGI FIGPSP
Sbjct: 97 AGITFIGPSP 106
>gnl|CDD|79056 PRK12581, PRK12581, oxaloacetate decarboxylase; Provisional.
Length = 468
Score = 101 bits (252), Expect = 2e-22
Identities = 83/281 (29%), Positives = 131/281 (46%), Gaps = 14/281 (4%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
DMAG+L P+AAK L+ I+ ++P+ +HTH TSG + +A EAGAD +D A+
Sbjct: 184 DMAGILTPKAAKELVSGIKAM-TNLPLIVHTHATSGISQMTYLAAVEAGADRIDTALSPF 242
Query: 530 SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLY-APFECTTTMKSGNAD 588
S TSQP+ ++ +L+ + D LD + + + Q RQ Y A ++ +
Sbjct: 243 SEGTSQPATESMYLALKEAGYDITLDETLLEQAANHLRQARQKYLADGILDPSLLFPDPR 302
Query: 589 VYLNEIPGGQYTNLQFQAYSLGLGEFFEDVKKAYREANLLLGDIIKVTPSSKVVGDFAQF 648
++PGG +N+ Q E+V LG VTP S++VG A
Sbjct: 303 TLQYQVPGGMLSNMLSQLKQANAESKLEEVLAEVPRVRKDLGYPPLVTPLSQMVGTQAAM 362
Query: 649 MVQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLRSKVLKDMPRIEGRPGA 708
V +L + ++ K + ++L G G E L+ + P RP
Sbjct: 363 NV--------ILGKPYQM-VSKEIKQYLAGDYGKTPAPVNEDLKRSQIGSAPVTTNRPAD 413
Query: 709 SLPPFDFGKLKTELQERHPEATDRDVMSAALYPQVTEDYLT 749
L P +F LK E+ + TD DV++ AL+P V + +LT
Sbjct: 414 QLSP-EFEVLKAEVADL--AQTDEDVLTYALFPSVAKPFLT 451
Score = 97.5 bits (242), Expect = 5e-21
Identities = 46/97 (47%), Positives = 63/97 (64%), Gaps = 2/97 (2%)
Query: 805 KSLLLMDTTFRDAHQSLLATRVRSHDLLKISPFVAHKFNNLYSLENWGGATFDVALRFLH 864
+ + + +T RD HQSL+ATR+ D+L + + YSLE WGGATFD +RFL+
Sbjct: 11 QQVAITETVLRDGHQSLMATRLSIEDMLPVLTILDKI--GYYSLECWGGATFDACIRFLN 68
Query: 865 ECPWERLEEMRKQIPNIPFQMLLRGANAVGYTNYPDN 901
E PWERL ++K +PN QMLLRG N +GY +Y D+
Sbjct: 69 EDPWERLRTLKKGLPNTRLQMLLRGQNLLGYRHYADD 105
Score = 78.6 bits (193), Expect = 5e-15
Identities = 43/101 (42%), Positives = 59/101 (58%), Gaps = 6/101 (5%)
Query: 969 MLLRGANAVGYTNYPDNVVYKFCDLSVQVGMDVFRVFDSLNYLPNLILGMEAAGKAGGVV 1028
MLLRG N +GY +Y D++V KF LS Q G+DVFR+FD+LN N+ + A K G
Sbjct: 89 MLLRGQNLLGYRHYADDIVDKFISLSAQNGIDVFRIFDALNDPRNIQQALRAVKKTGKEA 148
Query: 1029 EAAISYTGDVSDPSKKKYDLKYYQNLADELVKAGTHVLCIK 1069
+ I+YT + + L YY +L ELV+ G +CIK
Sbjct: 149 QLCIAYT------TSPVHTLNYYLSLVKELVEMGADSICIK 183
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 95.1 bits (237), Expect = 1e-19
Identities = 81/307 (26%), Positives = 134/307 (43%), Gaps = 38/307 (12%)
Query: 56 AQAVLDAGIRFIGPSPYVVQQMGDKVAARQAAIDS-GVPIVPGTPGPITTTEEAMEFCLK 114
A+A+ +AG+ +G SP + + D+ +D G+P T+ EEA+EF +
Sbjct: 646 AKALEEAGVPILGTSPESIDRAEDR-EKFSELLDELGIPQPKW--KTATSVEEAVEFASE 702
Query: 115 YGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIE 174
G PV+ + +Y GGR M +V E++ + A + + I+K++E ++
Sbjct: 703 IGYPVLVRPSYVLGGRAMEIVYNEEELRRYLEEAVEVSP----EHPVLIDKYLEDAVEVD 758
Query: 175 VQLLGD--------------KAGNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMT 220
V + D +AG VH + C + P L + +++
Sbjct: 759 VDAVSDGEEVLIPGIMEHIEEAG--VHSGDSTCVL-----------PPQTLSAEIVDRIK 805
Query: 221 DLAVKLAKHVGYSNAGTVEFLCDESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVA 280
D+ K+AK + ++F + G+ Y IEVN R + TGV L++ RV
Sbjct: 806 DIVRKIAKELNVKGLMNIQFAVKD-GEVYVIEVNPRASRTVPFVSKATGVPLIKLATRVM 864
Query: 281 EGMTLPELGLTQEKISPQGFAIQCRVTTEDPAKNFQPDTGRIEVFRSGEGMGIRLDGASA 340
G L ELG+ +EK A++ V + P G E+ +GE MGI D A A
Sbjct: 865 LGKKLEELGVGKEKEPK-YVAVKEPVFSFSKLAGVDPVLG-PEMKSTGEVMGIGRDLAEA 922
Query: 341 FAGAIIS 347
F A +S
Sbjct: 923 FLKAQLS 929
Score = 71.2 bits (175), Expect = 3e-12
Identities = 72/299 (24%), Positives = 132/299 (44%), Gaps = 43/299 (14%)
Query: 8 ADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYG---------FLSERSDFAQA 58
AD+ Y+ P+ + +II KE DAI P +G L E
Sbjct: 60 ADKVYIE-----PLTPE-AVEKIIE--KER-PDAILPTFGGQTALNLAVELEES-----G 105
Query: 59 VLDA-GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGL 117
VL+ G+ +G +++ D+ R+A + G P+ + EEA+ + G
Sbjct: 106 VLEKYGVEVLGTPVEAIKKAEDRELFREAMKEIGEPVPES--EIAHSVEEALAAAKEIGY 163
Query: 118 PVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQL 177
PVI + A+ GG G + E+++E +RA S + + +EK + + IE ++
Sbjct: 164 PVIVRPAFTLGGTGGGIAYNREELKEIAERALSASPI----NQVLVEKSLAGWKEIEYEV 219
Query: 178 LGDKAGNVVHLYERDCSVQR-----RH--QKVVEIAPAPHLDINVRNKMTDLAVKLAKHV 230
+ D N + + C+++ H +V +AP+ L + D ++K+ + +
Sbjct: 220 MRDSNDNCITV----CNMENFDPMGVHTGDSIV-VAPSQTLTDKEYQMLRDASIKIIREL 274
Query: 231 GYSNAGTVEFLCD-ESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPEL 288
G V+F + +SG++Y IEVN R+ + + TG + + ++A G L EL
Sbjct: 275 GIEGGCNVQFALNPDSGRYYVIEVNPRVSRSSALASKATGYPIAKVAAKLAVGYGLDEL 333
>gnl|CDD|133459 cd06850, biotinyl_domain, The biotinyl-domain or biotin carboxyl
carrier protein (BCCP) domain is present in all
biotin-dependent enzymes, such as acetyl-CoA
carboxylase, pyruvate carboxylase, propionyl-CoA
carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA
carboxylase, oxaloacetate decarboxylase,
methylmalonyl-CoA decarboxylase, transcarboxylase and
urea amidolyase. This domain functions in transferring
CO2 from one subsite to another, allowing carboxylation,
decarboxylation, or transcarboxylation. During this
process, biotin is covalently attached to a specific
lysine.
Length = 67
Score = 80.9 bits (201), Expect = 8e-19
Identities = 32/50 (64%), Positives = 37/50 (74%)
Query: 916 QVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
+V APMPG+V+++ VK GDKVE G L VL AMKME V APV GVVK I
Sbjct: 1 EVTAPMPGTVVKVLVKEGDKVEAGQPLAVLEAMKMENEVTAPVAGVVKEI 50
Score = 33.5 bits (78), Expect = 0.049
Identities = 17/30 (56%), Positives = 21/30 (70%)
Query: 916 QVGAPMPGSVMEIRVKVGDKVEKGAALVVL 945
+V AP+ G V EI VK GD+VE G LVV+
Sbjct: 38 EVTAPVAGVVKEILVKEGDQVEAGQLLVVI 67
>gnl|CDD|223534 COG0458, CarB, Carbamoylphosphate synthase large subunit (split
gene in MJ) [Amino acid transport and metabolism /
Nucleotide transport and metabolism].
Length = 400
Score = 82.8 bits (205), Expect = 1e-16
Identities = 68/292 (23%), Positives = 124/292 (42%), Gaps = 30/292 (10%)
Query: 8 ADESYLVGKGLPPVEAYLNIPEII-RVAKENDVDAIHPGYG------FLSERSDFAQAVL 60
AD+ Y+ P+ E + ++ ++ DAI P G E + + VL
Sbjct: 49 ADKVYIE-----PI-----TKEPVEKIIEKERPDAILPTLGGQTALNAALELKE--KGVL 96
Query: 61 DA-GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPV 119
+ G+ +G P ++ DK ++A + G+P+ + EEA E + G PV
Sbjct: 97 EKYGVEVVGSDPEAIEIAEDKKLFKEAMREIGIPVPSRIA---HSVEEADEIADEIGYPV 153
Query: 120 IFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLG 179
I K ++G GG G + E++EE E A + IE+ I + E +++
Sbjct: 154 IVKPSFGLGGSGGGIAYNEEELEE----IIEEGLRASPVEEVLIEESIIGWKEFEYEVVR 209
Query: 180 DKAGNVVHLYER-DCSVQRRH-QKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGT 237
D N + + + H + +APA L + D A+K+ + +G
Sbjct: 210 DGKDNCIVVCNMENLDPMGVHTGDSITVAPAQTLTDKEYQMLRDAAIKVIREIGIEGGCN 269
Query: 238 VEF-LCDESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPEL 288
++F + G+ Y IE+N R+ + + TG + + ++A G TL E+
Sbjct: 270 IQFAVDPGGGELYVIEINPRVSRSSALASKATGYPIAKVAAKLAVGYTLDEI 321
>gnl|CDD|237215 PRK12815, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1068
Score = 77.7 bits (192), Expect = 3e-14
Identities = 78/308 (25%), Positives = 126/308 (40%), Gaps = 51/308 (16%)
Query: 56 AQAVLDAGIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKY 115
A+ + +AG+ +G SP + ++ D+ Q + G+P VPG T EEA F +
Sbjct: 647 AKGLEEAGLTILGTSPDTIDRLEDRDRFYQLLDELGLPHVPG--LTATDEEEAFAFAKRI 704
Query: 116 GLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEV 175
G PV+ + +Y GG+GM VV +E +S + I++FI+ + EV
Sbjct: 705 GYPVLIRPSYVIGGQGMAVVYDEPALEAYLAENAS------QLYPILIDQFID-GKEYEV 757
Query: 176 QLLGD--------------KAGNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTD 221
+ D +AG VH + + P L + K+ D
Sbjct: 758 DAISDGEDVTIPGIIEHIEQAG--VHSGDSIA-----------VLPPQSLSEEQQEKIRD 804
Query: 222 LAVKLAKHVGYSNAGTVEFLCDESGQFYFIEVNARLQVEHTV--TEEITGVDLVQSQIRV 279
A+K+AK +G+ ++F+ + Y +EVN R TV + TGV L + +V
Sbjct: 805 YAIKIAKKLGFRGIMNIQFVLAN-DEIYVLEVNPR--ASRTVPFVSKATGVPLAKLATKV 861
Query: 280 AEGMTLPELGLTQEKISPQGFAIQCRVTTEDPAKNFQ--PDTGRI---EVFRSGEGMGIR 334
G +L ELG F + + P ++ P E+ +GE MGI
Sbjct: 862 LLGKSLAELGYPNGLWPGSPF-----IHVKMPVFSYLKYPGVDNTLGPEMKSTGEVMGID 916
Query: 335 LDGASAFA 342
D A
Sbjct: 917 KDLEEALY 924
Score = 47.7 bits (114), Expect = 4e-05
Identities = 63/249 (25%), Positives = 113/249 (45%), Gaps = 26/249 (10%)
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFK 122
G+ +G + +Q+ D+ R + G P VP + +T+ EEA+ F K G P+I +
Sbjct: 112 GVELLGTNIEAIQKGEDRERFRALMKELGEP-VPES-EIVTSVEEALAFAEKIGFPIIVR 169
Query: 123 AAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKA 182
AY GG G + +E++E+ F++ + +E+ I + IE +++ D+
Sbjct: 170 PAYTLGGTGGGIAENLEELEQLFKQGLQA--SPIHQ--CLLEESIAGWKEIEYEVMRDRN 225
Query: 183 GNVVHLYERDCS--------VQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSN 234
GN + + C+ + VV AP+ L + + ++K+ +G
Sbjct: 226 GNCITV----CNMENIDPVGIHTGDSIVV--APSQTLTDDEYQMLRSASLKIISALGVVG 279
Query: 235 AGTVEFLCD-ESGQFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTLPEL----- 288
++F D +S Q+Y IEVN R+ + + TG + + ++A G TL EL
Sbjct: 280 GCNIQFALDPKSKQYYLIEVNPRVSRSSALASKATGYPIAKIAAKLAVGYTLNELKNPVT 339
Query: 289 GLTQEKISP 297
GLT P
Sbjct: 340 GLTYASFEP 348
Score = 30.3 bits (69), Expect = 6.7
Identities = 28/115 (24%), Positives = 42/115 (36%), Gaps = 13/115 (11%)
Query: 747 YLTFRESFGPVDKLDTRIFLTGP--KVGEEFEVKIQPPQGFRQ-ILKSKGPEAFAKAVRQ 803
F + L T++ TG +G FE Q + R +K G + +
Sbjct: 359 RWPFDKFGYADRTLGTQMKATGEVMAIGRNFESAFQ--KALRSLEIKRNGLSLPIELSGK 416
Query: 804 NKSLLLMD-TTFRDAHQSLLATRVRS-------HDLLKISPFVAHKFNNLYSLEN 850
+ LL D D L +R H+L KI PF KF ++ +LE
Sbjct: 417 SDEELLQDLRHPDDRRLFALLEALRRGITYEEIHELTKIDPFFLQKFEHIVALEK 471
>gnl|CDD|223585 COG0511, AccB, Biotin carboxyl carrier protein [Lipid metabolism].
Length = 140
Score = 70.5 bits (173), Expect = 3e-14
Identities = 27/57 (47%), Positives = 37/57 (64%)
Query: 909 AAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
AA + QV +PM G+V + V+VGD V+ G L ++ AMKME ++AP GVVK I
Sbjct: 65 AAAAGGTQVTSPMVGTVYKPFVEVGDTVKAGQTLAIIEAMKMENEIEAPADGVVKEI 121
Score = 33.5 bits (77), Expect = 0.18
Identities = 15/32 (46%), Positives = 18/32 (56%)
Query: 916 QVGAPMPGSVMEIRVKVGDKVEKGAALVVLSA 947
++ AP G V EI VK GD VE G L V+
Sbjct: 109 EIEAPADGVVKEILVKNGDPVEYGDPLAVIEP 140
>gnl|CDD|201182 pfam00364, Biotin_lipoyl, Biotin-requiring enzyme. This family
covers two Prosite entries, the conserved lysine residue
binds biotin in one group and lipoic acid in the other.
Note that the HMM does not currently recognise the
Glycine cleavage system H proteins.
Length = 73
Score = 67.6 bits (166), Expect = 5e-14
Identities = 27/55 (49%), Positives = 34/55 (61%), Gaps = 5/55 (9%)
Query: 916 QVGAPMPGSVM-----EIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
++ +PM G + E VKVGDKV+ G L + AMKMEM + APV GVVK I
Sbjct: 2 EIKSPMIGESVKEGTAEWLVKVGDKVKAGQVLCEVEAMKMEMEIPAPVAGVVKEI 56
Score = 31.0 bits (71), Expect = 0.44
Identities = 14/27 (51%), Positives = 16/27 (59%)
Query: 919 APMPGSVMEIRVKVGDKVEKGAALVVL 945
AP+ G V EI VK GD VE G L +
Sbjct: 47 APVAGVVKEILVKEGDTVEVGDPLAKI 73
>gnl|CDD|222206 pfam13535, ATP-grasp_4, ATP-grasp domain. This family includes a
diverse set of enzymes that possess ATP-dependent
carboxylate-amine ligase activity.
Length = 183
Score = 70.8 bits (174), Expect = 6e-14
Identities = 37/185 (20%), Positives = 71/185 (38%), Gaps = 16/185 (8%)
Query: 79 DKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKM 138
DK R+ +G+P+ P + E+ + G PV+ K G G G+ V
Sbjct: 4 DKALMRELLRAAGLPVPPFFL--VDDEEDLDAAAEEIGFPVVLKPRDGAGSLGVFRVDSA 61
Query: 139 EDVEENFQRASSEAKAAFGNGAMFIEKFIERP-RHIEVQLLGDKAGNVVHL----YERDC 193
++E ++E +E++I+ H++ + G +V L Y
Sbjct: 62 AELEAALAALAAE---VEDTREYLVEEYIDGDEYHVDGLVDD---GELVFLGVSRYLGPP 115
Query: 194 SVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGT-VEFLCDESGQFYFIE 252
+ VE+ + + + +LA ++ K +G N +EF G+ +E
Sbjct: 116 PP--DFSEGVELGSVSPGEDPLPEALRELAERVLKALGLRNGVFHLEFFLTPDGRPVLLE 173
Query: 253 VNARL 257
+N R
Sbjct: 174 INPRP 178
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 67.7 bits (166), Expect = 2e-12
Identities = 29/82 (35%), Positives = 46/82 (56%)
Query: 466 INTFDMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVA 525
IN D G+L P A LI A++++ P + I +H H+ G VA+ +A EAGAD VD
Sbjct: 153 INIADTVGVLTPNEAADLISALKDRVPPVIIEVHCHNDLGMAVANSLAAVEAGADRVDGT 212
Query: 526 VDSMSGMTSQPSMGAVVASLQG 547
V+ + ++ +VA+L+
Sbjct: 213 VNGLGERAGNAALEELVAALEV 234
>gnl|CDD|233310 TIGR01205, D_ala_D_alaTIGR, D-alanine--D-alanine ligase. This
model describes D-Ala--D-Ala ligase, an enzyme that
makes a required precursor of the bacterial cell wall.
It also describes some closely related proteins
responsible for resistance to glycopeptide antibiotics
such as vancomycin. The mechanism of glyopeptide
antibiotic resistance involves the production of
D-alanine-D-lactate (VanA and VanB families) or
D-alanine-D-serine (VanC). The seed alignment contains
only chromosomally encoded D-ala--D-ala ligases, but a
number of antibiotic resistance proteins score above the
trusted cutoff of this model [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 315
Score = 65.8 bits (161), Expect = 3e-11
Identities = 55/218 (25%), Positives = 88/218 (40%), Gaps = 37/218 (16%)
Query: 57 QAVLD-AGIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTP--GPITTTEEA--MEF 111
Q +L+ GI + G DK+ + G+P + +E +
Sbjct: 82 QGLLELMGIPYTGSGVLASALSMDKLLTKLLWKALGLPTPDYIVLTQNRASADELECEQV 141
Query: 112 CLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFG-NGAMFIEKFIERP 170
G PVI K A G G+ V+ EE Q A AF + + +E+FI+
Sbjct: 142 AEPLGFPVIVKPAREGSSVGVSKVKS----EEELQAA---LDEAFEYDEEVLVEQFIK-G 193
Query: 171 RHIEVQLLG-DKAGNVVHL-------------YERDCSVQRRHQKVVEIAPAPHLDINVR 216
R +EV +LG ++A ++ + Y + V+ PAP LD +
Sbjct: 194 RELEVSILGNEEALPIIEIVPEIEGFYDYEAKYLDG-----STEYVI---PAP-LDEELE 244
Query: 217 NKMTDLAVKLAKHVGYSNAGTVEFLCDESGQFYFIEVN 254
K+ +LA+K K +G V+F DE G+ Y E+N
Sbjct: 245 EKIKELALKAYKALGCRGLARVDFFLDEEGEIYLNEIN 282
>gnl|CDD|235540 PRK05641, PRK05641, putative acetyl-CoA carboxylase biotin carboxyl
carrier protein subunit; Validated.
Length = 153
Score = 60.6 bits (147), Expect = 1e-10
Identities = 27/59 (45%), Positives = 36/59 (61%)
Query: 907 PKAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
P A + V APMPG ++ I V+ G +V+ G L++L AMKME + AP GVVK I
Sbjct: 77 PAPASAGENVVTAPMPGKILRILVREGQQVKVGQGLLILEAMKMENEIPAPKDGVVKKI 135
>gnl|CDD|237195 PRK12767, PRK12767, carbamoyl phosphate synthase-like protein;
Provisional.
Length = 326
Score = 63.0 bits (154), Expect = 3e-10
Identities = 55/267 (20%), Positives = 105/267 (39%), Gaps = 54/267 (20%)
Query: 6 QKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGY----GFLSE-RSDFAQAVL 60
AD+ Y+V P V I ++ + K+ +D + P L++ R F
Sbjct: 41 YFADKFYVV----PKVTDPNYIDRLLDICKKEKIDLLIPLIDPELPLLAQNRDRFE---- 92
Query: 61 DAGIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAME------FCLK 114
+ G++ + S V++ DK + ++G+P P + E++E +
Sbjct: 93 EIGVKVLVSSKEVIEICNDKWLTYEFLKENGIPT------PKSYLPESLEDFKAALAKGE 146
Query: 115 YGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIE 174
P+ K G G+ V E++E + + I++FIE E
Sbjct: 147 LQFPLFVKPRDGSASIGVFKVNDKEELEFLLEY----------VPNLIIQEFIE---GQE 193
Query: 175 --VQLLGDKAGNVVHLYERDCSVQRRHQKVV--EIAPAPHLDINVRN-KMTDLAVKLAKH 229
V +L D G V+ V R+ +V E + + V++ ++ LA +LA+
Sbjct: 194 YTVDVLCDLNGEVIS------IVPRKRIEVRAGETSKG----VTVKDPELFKLAERLAEA 243
Query: 230 VGYSNAGTVEFLCDESGQFYFIEVNAR 256
+G ++ + G+ Y E+N R
Sbjct: 244 LGARGPLNIQCFVTD-GEPYLFEINPR 269
>gnl|CDD|181304 PRK08225, PRK08225, acetyl-CoA carboxylase biotin carboxyl carrier
protein subunit; Validated.
Length = 70
Score = 56.3 bits (136), Expect = 4e-10
Identities = 25/50 (50%), Positives = 34/50 (68%)
Query: 916 QVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
+V A M G+V +I VKVGD VE+G +V+L +MKME+ + A G VK I
Sbjct: 3 KVYASMAGNVWKIVVKVGDTVEEGQDVVILESMKMEIPIVAEEAGTVKKI 52
>gnl|CDD|216935 pfam02222, ATP-grasp, ATP-grasp domain. This family does not
contain all known ATP-grasp domain members. This family
includes a diverse set of enzymes that possess
ATP-dependent carboxylate-amine ligase activity.
Length = 171
Score = 57.6 bits (140), Expect = 2e-09
Identities = 38/161 (23%), Positives = 62/161 (38%), Gaps = 19/161 (11%)
Query: 101 PITTTEEAMEFCLKYGLPVIFKAAYGG-GGRGMRVVRKMEDVEENFQRASSEAKAAFGNG 159
+ EE +E + G P + KA GG G+G VVR D+ + A G G
Sbjct: 13 AAESLEELIEAGQELGYPCVLKARRGGYDGKGQYVVRSEADIPQ--------AWEELGGG 64
Query: 160 AMFIEKFIERPRHIEVQLLGDKAGN-VVHLYERDCSVQRRHQK---VVEIAPAPHLDINV 215
+ +E+F+ P E+ +L ++ + Y V+ + +APA D
Sbjct: 65 PVIVEEFV--PFDKELSVLVVRSVDGETAFYP---PVETIQEDGICRESVAPARVPDSQQ 119
Query: 216 RNKMTDLAVKLAKHVGYSNAGTVEFLCDESGQFYFIEVNAR 256
K ++A K+ +G VE G E+ R
Sbjct: 120 A-KAQEIAKKIVDELGGVGIFGVELFVLPDGDLLVNELAPR 159
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 60.5 bits (148), Expect = 4e-09
Identities = 75/265 (28%), Positives = 114/265 (43%), Gaps = 43/265 (16%)
Query: 56 AQAVLDAGIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKY 115
A+A+ AG+ +G SP + D+ + G+P P G T+ EEA+E +
Sbjct: 646 AKALEAAGVPILGTSPDAIDLAEDRERFSKLLEKLGIPQPPN--GTATSVEEALEVAEEI 703
Query: 116 GLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEV 175
G PV+ + +Y GGR M +V E++E + EA + + I+KF+E ++V
Sbjct: 704 GYPVLVRPSYVLGGRAMEIVYDEEELERYMR----EAVKVSPDHPVLIDKFLEGAIEVDV 759
Query: 176 QLLGDK-----AGNVVHLYER------D--CSVQRRHQKVVEIAPAPHLDINVRNKMTDL 222
+ D G + H+ E D CS+ P L + ++ +
Sbjct: 760 DAICDGEDVLIGGIMEHI-EEAGVHSGDSACSL-----------PPQTLSEEIIEEIREY 807
Query: 223 AVKLAKH---VGYSNAGTVEFLCDESGQFYFIEVNARLQVEHTV--TEEITGVDLVQSQI 277
KLA VG N V+F + + Y IEVN R TV + TGV L +
Sbjct: 808 TKKLALELNVVGLMN---VQFAVKD-DEVYVIEVNPR--ASRTVPFVSKATGVPLAKIAA 861
Query: 278 RVAEGMTLPELGLTQEKISPQGFAI 302
RV G L ELG T+ I P A+
Sbjct: 862 RVMLGKKLAELGYTKGLI-PPYVAV 885
Score = 44.7 bits (107), Expect = 3e-04
Identities = 43/173 (24%), Positives = 73/173 (42%), Gaps = 30/173 (17%)
Query: 27 IPEIIRVAKENDVDAIHPGYG---------FLSERSDFAQAVLDA-GIRFIGPSPYVVQQ 76
+ +II KE DAI P G L+E VL+ G+ IG + +
Sbjct: 74 VEKIIE--KER-PDAILPTMGGQTALNLAVELAE-----SGVLEKYGVELIGAKLEAIDK 125
Query: 77 MGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVR 136
D+ ++A G+P+ G + EEA+E + G PVI + ++ GG G +
Sbjct: 126 AEDRELFKEAMKKIGLPVPRS--GIAHSMEEALEVAEEIGYPVIIRPSFTLGGTGGGIAY 183
Query: 137 KMEDVEENFQR---ASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVV 186
E++EE +R S + IE+ + + E +++ DK N +
Sbjct: 184 NEEELEEIVERGLDLSP-------VTEVLIEESLLGWKEYEYEVMRDKNDNCI 229
>gnl|CDD|215391 PLN02735, PLN02735, carbamoyl-phosphate synthase.
Length = 1102
Score = 60.6 bits (147), Expect = 4e-09
Identities = 69/273 (25%), Positives = 106/273 (38%), Gaps = 51/273 (18%)
Query: 99 PGPITTTE-EAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMED--------VEENFQRAS 149
G I +E +A+ + G PV+ + +Y GGR M +V + VE + +R
Sbjct: 719 KGGIARSEADALAIAKRIGYPVVVRPSYVLGGRAMEIVYSDDKLKTYLETAVEVDPER-- 776
Query: 150 SEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVV-------------HLYERDCSVQ 196
+ ++K++ I+V L D GNVV H + CS+
Sbjct: 777 ----------PVLVDKYLSDATEIDVDALADSEGNVVIGGIMEHIEQAGVHSGDSACSL- 825
Query: 197 RRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLCDESGQFYFIEVNAR 256
P + + + D KLAK + ++ SG+ Y IE N R
Sbjct: 826 ----------PTQTIPSSCLATIRDWTTKLAKRLNVCGLMNCQYAITPSGEVYIIEANPR 875
Query: 257 LQVEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAIQCRVTTEDPAKNFQ 316
+ G L + V G +L +LG T+E I P +++ V P FQ
Sbjct: 876 ASRTVPFVSKAIGHPLAKYASLVMSGKSLKDLGFTEEVI-PAHVSVKEAVL---PFDKFQ 931
Query: 317 -PDTGRIEVFRS-GEGMGIRLDGASAFAGAIIS 347
D RS GE MGI + + AFA A I+
Sbjct: 932 GCDVLLGPEMRSTGEVMGIDYEFSKAFAKAQIA 964
Score = 44.4 bits (105), Expect = 4e-04
Identities = 67/279 (24%), Positives = 119/279 (42%), Gaps = 37/279 (13%)
Query: 28 PEIIR--VAKENDVDAIHPGYG---------FLSERSDFAQAVLDA-GIRFIGPSPYVVQ 75
PE++ +AKE DA+ P G L+E +L+ G+ IG ++
Sbjct: 87 PELVEQVIAKERP-DALLPTMGGQTALNLAVALAES-----GILEKYGVELIGAKLDAIK 140
Query: 76 QMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYG-LPVIFKAAYGGGGRGMRV 134
+ D+ +QA G+ P G TT +E E G P+I + A+ GG G +
Sbjct: 141 KAEDRELFKQAMEKIGLKTPPS--GIATTLDECFEIAEDIGEFPLIIRPAFTLGGTGGGI 198
Query: 135 VRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVVHLYERDCS 194
E+ F+ AA + +EK + + E++++ D A NVV + CS
Sbjct: 199 AYNKEE----FETICKAGLAASITSQVLVEKSLLGWKEYELEVMRDLADNVVII----CS 250
Query: 195 VQRRHQKVVE------IAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGT-VEFLCD-ESG 246
++ V +APA L ++ D +V + + +G G+ V+F + G
Sbjct: 251 IENIDPMGVHTGDSITVAPAQTLTDKEYQRLRDYSVAIIREIGVECGGSNVQFAVNPVDG 310
Query: 247 QFYFIEVNARLQVEHTVTEEITGVDLVQSQIRVAEGMTL 285
+ IE+N R+ + + TG + + +++ G TL
Sbjct: 311 EVMIIEMNPRVSRSSALASKATGFPIAKMAAKLSVGYTL 349
>gnl|CDD|203643 pfam07478, Dala_Dala_lig_C, D-ala D-ala ligase C-terminus. This
family represents the C-terminal, catalytic domain of
the D-alanine--D-alanine ligase enzyme EC:6.3.2.4.
D-Alanine is one of the central molecules of the
cross-linking step of peptidoglycan assembly. There are
three enzymes involved in the D-alanine branch of
peptidoglycan biosynthesis: the pyridoxal
phosphate-dependent D-alanine racemase (Alr), the
ATP-dependent D-alanine:D-alanine ligase (Ddl), and the
ATP-dependent D-alanine:D-alanine-adding enzyme (MurF).
Length = 201
Score = 57.3 bits (139), Expect = 4e-09
Identities = 42/156 (26%), Positives = 64/156 (41%), Gaps = 23/156 (14%)
Query: 110 EFCLKYGLPVIFKAAYGGGGRGMRVVRKMED----VEENFQRASSEAKAAFGNGAMFIEK 165
+ K G PV K A G G+ V E+ +EE FQ + + IE+
Sbjct: 27 KVEEKLGYPVFVKPANLGSSVGISKVTSREELQSAIEEAFQYDN----------KVLIEE 76
Query: 166 FIERPRHIEVQLLGDKAGNVVHLYER--DCSVQRRHQKVVEIA-----PAPHLDINVRNK 218
IE R IE +LG++ V + E K ++ + PA L V +
Sbjct: 77 AIE-GREIECAVLGNEDLEVSPVGEIRLSGGFYDYEAKYIDSSAQIIVPA-DLPEEVEEQ 134
Query: 219 MTDLAVKLAKHVGYSNAGTVEFLCDESGQFYFIEVN 254
+ +LA+K K +G ++F E G+ Y EVN
Sbjct: 135 IQELALKAYKALGCRGLARIDFFLTEDGEIYLNEVN 170
>gnl|CDD|235674 PRK06019, PRK06019, phosphoribosylaminoimidazole carboxylase ATPase
subunit; Reviewed.
Length = 372
Score = 57.5 bits (140), Expect = 2e-08
Identities = 51/195 (26%), Positives = 83/195 (42%), Gaps = 32/195 (16%)
Query: 69 PSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGG- 127
P P + D++ +Q G+P+ P + + E+ GLP + K GG
Sbjct: 90 PGPDALAIAQDRLTEKQFLDKLGIPVAPFAV--VDSAEDLEAALADLGLPAVLKTRRGGY 147
Query: 128 GGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFI--ERPRHIEVQLLG--DKAG 183
G+G V+R ED+E A A G+ +E+F+ ER EV ++ + G
Sbjct: 148 DGKGQWVIRSAEDLE--------AAWALLGSVPCILEEFVPFER----EVSVIVARGRDG 195
Query: 184 NVVH--LYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGT--VE 239
VV L E +V R IAPA + ++ + ++A ++A+ + Y G VE
Sbjct: 196 EVVFYPLVE---NVHRNGILRTSIAPA-RISAELQAQAEEIASRIAEELDYV--GVLAVE 249
Query: 240 FLCDESGQFYFIEVN 254
F G+ VN
Sbjct: 250 FFVTGDGELL---VN 261
>gnl|CDD|234948 PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed.
Length = 304
Score = 56.7 bits (138), Expect = 2e-08
Identities = 49/188 (26%), Positives = 86/188 (45%), Gaps = 30/188 (15%)
Query: 79 DKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKM 138
DK+ + +G+P P +T E+ + K GLP++ K A G G+ V++
Sbjct: 98 DKLRTKLVWQAAGLPTPPW--IVLTREEDLLAAIDKLGLPLVVKPAREGSSVGVSKVKE- 154
Query: 139 EDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVVHL---------- 188
E+ Q A A + + + +EK+I+ R + V +LG KA V+ +
Sbjct: 155 ---EDELQAALELA-FKYDDEVL-VEKYIK-GRELTVAVLGGKALPVIEIVPAGEFYDYE 208
Query: 189 --YERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLCDESG 246
Y + ++ I PA L + ++ +LA+K + +G G V+F+ DE G
Sbjct: 209 AKYLAGGT---QY-----ICPAG-LPAEIEAELQELALKAYRALGCRGWGRVDFMLDEDG 259
Query: 247 QFYFIEVN 254
+ Y +EVN
Sbjct: 260 KPYLLEVN 267
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 56.5 bits (137), Expect = 4e-08
Identities = 30/114 (26%), Positives = 55/114 (48%), Gaps = 4/114 (3%)
Query: 466 INTFDMAGLLKPRAAKLLIGAIREK-HPDIPIHIHTHDTSGAGVASMIACAEAGADVVDV 524
IN D G+ P +I A++ + + +H H+ G VA+ +A EAGAD V+
Sbjct: 163 INLPDTVGVATPNEVADIIEALKANVPNKVILSVHCHNDLGMAVANSLAAVEAGADQVEG 222
Query: 525 AVDSM---SGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYSAYWEQTRQLYAP 575
V+ + +G + + +A + +DTG+DL+ ++ S E+ + P
Sbjct: 223 TVNGIGERAGNAALEEVVLALALRKDYGVDTGIDLEKLTEASRLVERLTGIPVP 276
>gnl|CDD|233121 TIGR00768, rimK_fam, alpha-L-glutamate ligases, RimK family. This
family, related to bacterial glutathione synthetases,
contains at least two different alpha-L-glutamate
ligases. One is RimK, as in E. coli, which adds
additional Glu residues to the native Glu-Glu C-terminus
of ribosomal protein S6, but not to Lys-Glu mutants.
Most species with a member of this subfamily lack an S6
homolog ending in Glu-Glu, however. Members in
Methanococcus jannaschii act instead as a
tetrahydromethanopterin:alpha-l-glutamate ligase
(MJ0620) and a gamma-F420-2:alpha-l-glutamate ligase
(MJ1001).
Length = 277
Score = 55.4 bits (134), Expect = 4e-08
Identities = 63/282 (22%), Positives = 107/282 (37%), Gaps = 39/282 (13%)
Query: 3 MHRQKADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDA 62
M ++ A+E + K + P L E R + ++D + + A+ +
Sbjct: 15 MLKEAAEELGIDYKVVTPPAIPLTFNEGPR--ELAELDVVIVRIVSMFRGLAVARYLESL 72
Query: 63 GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTT----EEAMEFCLKYGLP 118
G+ I + GDK Q +G+P P T EEA++ + G P
Sbjct: 73 GVPVINS-SDAILNAGDKFLTSQLLAKAGLPQ------PRTGLAGSPEEALKLIEEIGFP 125
Query: 119 VIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGN--GAMFIEKFIERP--RHIE 174
V+ K +G GR V D + E +++++I++P R I
Sbjct: 126 VVLKPVFGSWGRL---VSLARDKQA--AETLLEHFEQLNGPQNLFYVQEYIKKPGGRDIR 180
Query: 175 VQLLGDKAGNVVHLYERDCSVQRR---HQ-KVVEIAPAPHLDINVRNKMTDLAVKLAKHV 230
V ++GD+ V+ R S R + E P L + +LA+K AK +
Sbjct: 181 VFVVGDE---VIAAIYRITSGHWRTNLARGGKAEPCP---LTEEIE----ELAIKAAKAL 230
Query: 231 GYSNAGTVEFLCDESGQFYFIEVNARLQVEHTVTEEITGVDL 272
G G ++ L E EVN E + + TGV++
Sbjct: 231 GLDVVG-IDLLESEDRGLLVNEVNP--NPEFKNSVKTTGVNI 269
>gnl|CDD|224102 COG1181, DdlA, D-alanine-D-alanine ligase and related ATP-grasp
enzymes [Cell envelope biogenesis, outer membrane].
Length = 317
Score = 55.4 bits (134), Expect = 6e-08
Identities = 50/223 (22%), Positives = 80/223 (35%), Gaps = 40/223 (17%)
Query: 57 QAVLD-AGIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGT--PGPITTTEEAMEFCL 113
Q +L+ GI ++G DK+ ++ G+P+ P ++ E
Sbjct: 80 QGLLELLGIPYVGKGVLASAGAMDKIVTKRLFKAEGLPVAPYVALTRDEYSSVIVEEVEE 139
Query: 114 KYGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHI 173
G P+ K A G G V VE + Q A A + + E+ I R I
Sbjct: 140 GLGFPLFVKPAREGSSVGRSPVN----VEGDLQSALELAFKY--DRDVLREQGI-TGREI 192
Query: 174 EVQLLGD-------------KAGNVVHLYERDCSVQRRHQK------VVEIAPAPHLDIN 214
EV +LG+ G + YE K PA L
Sbjct: 193 EVGVLGNDYEEQALPLGEIPPKGEEFYDYE---------AKYLSTGGAQYDIPAG-LTDE 242
Query: 215 VRNKMTDLAVKLAKHVGYSNAGTVEFLC-DESGQFYFIEVNAR 256
+ ++ +LA++ K +G V+F D+ G+F +EVN
Sbjct: 243 IHEEIKELALRAYKALGCLGLARVDFFVDDDEGEFVLLEVNTN 285
>gnl|CDD|180306 PRK05889, PRK05889, putative acetyl-CoA carboxylase biotin carboxyl
carrier protein subunit; Provisional.
Length = 71
Score = 50.2 bits (120), Expect = 7e-08
Identities = 23/52 (44%), Positives = 32/52 (61%)
Query: 917 VGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSIDAS 968
V A + SV+E+ V GD++ KG LV+L +MKME+ V A V G V + S
Sbjct: 5 VRAEIVASVLEVVVNEGDQIGKGDTLVLLESMKMEIPVLAEVAGTVSKVSVS 56
>gnl|CDD|163676 cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase,
catalytic TIM barrel domain.
3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes
the cleavage of HMG-CoA to acetyl-CoA and acetoacetate,
one of the terminal steps in ketone body generation and
leucine degradation, and is a key enzyme in the pathway
that supplies metabolic fuel to extrahepatic tissues.
Mutations in HMGL cause a human autosomal recessive
disorder called primary metabolic aciduria that affects
ketogenesis and leucine catabolism and can be fatal due
to an inability to tolerate hypoglycemia. HMGL has a
TIM barrel domain with a catalytic center containing a
divalent cation-binding site formed by a cluster of
invariant residues that cap the core of the barrel. The
cleavage of HMG-CoA requires the presence of a divalent
cation like Mg2+ or Mn2+, and the reaction is thought to
involve general acid/base catalysis. This family
belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 274
Score = 54.7 bits (133), Expect = 8e-08
Identities = 30/90 (33%), Positives = 47/90 (52%), Gaps = 12/90 (13%)
Query: 477 PRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSMSGMTSQP 536
P + L+ A+ E+ PD + +H HDT G +A+++A EAG D +V G+ P
Sbjct: 177 PAQVRRLLEAVLERFPDEKLALHFHDTRGQALANILAALEAGVRRFDSSV---GGLGGCP 233
Query: 537 -SMGA--------VVASLQGSDIDTGLDLK 557
+ GA +V L+G I+TG+DL
Sbjct: 234 FAPGATGNVATEDLVYMLEGMGIETGIDLD 263
>gnl|CDD|235826 PRK06549, PRK06549, acetyl-CoA carboxylase biotin carboxyl carrier
protein subunit; Validated.
Length = 130
Score = 51.0 bits (122), Expect = 2e-07
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 907 PKAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSID 966
A ++P +PMPG+++++ V VGD+V + L++L AMKME + A G V +I
Sbjct: 58 AAGADAMP----SPMPGTILKVLVAVGDQVTENQPLLILEAMKMENEIVASSAGTVTAIH 113
Query: 967 AS 968
+
Sbjct: 114 VT 115
>gnl|CDD|223105 COG0026, PurK, Phosphoribosylaminoimidazole carboxylase (NCAIR
synthetase) [Nucleotide transport and metabolism].
Length = 375
Score = 51.1 bits (123), Expect = 2e-06
Identities = 41/191 (21%), Positives = 73/191 (38%), Gaps = 30/191 (15%)
Query: 69 PSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGG- 127
PSP ++ D++ +Q +G+P+ P + + EE G P + K GG
Sbjct: 89 PSPDALRIAQDRLVEKQFLDKAGLPVAPFQV--VDSAEELDAAAADLGFPAVLKTRRGGY 146
Query: 128 GGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLG--DKAGN- 184
G+G +R D+E A G +E+F+ R E+ ++ G
Sbjct: 147 DGKGQWRIRSDADLEL-------RAAGLAEGGVPVLEEFVPFER--EISVIVARSNDGEV 197
Query: 185 ----VVHLYERD--CSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTV 238
V R+ IAPA + +++ + ++A K+A+ + Y V
Sbjct: 198 AFYPVAENVHRNGIL--------RTSIAPA-RIPDDLQAQAEEMAKKIAEELDYVGVLAV 248
Query: 239 EFLCDESGQFY 249
EF G+
Sbjct: 249 EFFVTPDGELL 259
>gnl|CDD|163681 cd07943, DRE_TIM_HOA, 4-hydroxy-2-oxovalerate aldolase, N-terminal
catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate
aldolase (Also known as 4-hydroxy-2-ketovalerate
aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA))
converts 4-hydroxy-2-oxopentanoate to acetaldehyde and
pyruvate, the penultimate step in the meta-cleavage
pathway for the degradation of phenols, cresols and
catechol. This family includes the Escherichia coli
MhpE aldolase, the Pseudomonas DmpG aldolase, and the
Burkholderia xenovorans BphI pyruvate aldolase. In
Pseudomonas, the DmpG aldolase tightly associates with a
dehydrogenase (DmpF ) and is inactive without it. HOA
has a canonical TIM-barrel fold with a C-terminal
extension that forms a funnel leading to the active
site. This family belongs to the DRE-TIM metallolyase
superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 263
Score = 49.4 bits (119), Expect = 4e-06
Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 6/90 (6%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
D AG + P + + A+RE P+ H H+ G VA+ +A EAGA +D ++ +
Sbjct: 162 DSAGAMLPDDVRERVRALREALDPTPVGFHGHNNLGLAVANSLAAVEAGATRIDGSLAGL 221
Query: 530 ---SGMTSQPSMGAVVASLQGSDIDTGLDL 556
+G T + +VA L+ I+TG+DL
Sbjct: 222 GAGAGNT---PLEVLVAVLERMGIETGIDL 248
>gnl|CDD|131199 TIGR02144, LysX_arch, Lysine biosynthesis enzyme LysX. The family
of proteins found in this equivalog include the
characterized LysX from Thermus thermophilus which is
part of a well-organized lysine biosynthesis gene
cluster. LysX is believed to carry out an ATP-dependent
acylation of the amino group of alpha-aminoadipate in
the prokaryotic version of the fungal AAA lysine
biosynthesis pathway. No species having a sequence in
this equivalog contains the elements of the more common
diaminopimelate lysine biosythesis pathway, and none has
been shown to be a lysine auxotroph. These sequences
have mainly recieved the name of the related enzyme,
"ribosomal protein S6 modification protein RimK". RimK
has been characterized in E. coli, and acts by
ATP-dependent condensation of S6 with glutamate
residues.
Length = 280
Score = 48.9 bits (117), Expect = 6e-06
Identities = 57/221 (25%), Positives = 97/221 (43%), Gaps = 22/221 (9%)
Query: 56 AQAVLDAGIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKY 115
A+ + G+ I S +V++ GDK+ +GVP P T E A++
Sbjct: 65 ARLLEALGVPVINSS-HVIEACGDKIFTYLKLAKAGVPT-PRT-YLAFDREAALKLAEAL 121
Query: 116 GLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAM---FIEKFIERP-R 171
G PV+ K G G R+V + D +E + E K G +I+++I +P R
Sbjct: 122 GYPVVLKPVIGSWG---RLVALIRDKDE--LESLLEHKEVLGGSQHKLFYIQEYINKPGR 176
Query: 172 HIEVQLLGDKAGNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAKHVG 231
I V ++GD+A + +Y + + + P P LD V +LAVK A+ VG
Sbjct: 177 DIRVFVIGDEA--IAAIYRYSNHWRTNTARGGKAEPCP-LDEEVE----ELAVKAAEAVG 229
Query: 232 YSNAGTVEFLCDESGQFYFIEVNARLQVEHTVTEEITGVDL 272
++ + EVN + +++V +TGV++
Sbjct: 230 -GGVVAIDIFESKERGLLVNEVNHVPEFKNSV--RVTGVNV 267
>gnl|CDD|183341 PRK11858, aksA, trans-homoaconitate synthase; Reviewed.
Length = 378
Score = 49.0 bits (118), Expect = 8e-06
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAV 526
D G+L P L+ + + DIPI +H H+ G A+ +A EAGA V V
Sbjct: 166 DTVGILDPFTMYELVKELV-EAVDIPIEVHCHNDFGMATANALAGIEAGAKQVHTTV 221
>gnl|CDD|133456 cd06663, Biotinyl_lipoyl_domains, Biotinyl_lipoyl_domains are
present in biotin-dependent carboxylases/decarboxylases,
the dihydrolipoyl acyltransferase component (E2) of
2-oxo acid dehydrogenases, and the H-protein of the
glycine cleavage system (GCS). These domains transport
CO2, acyl, or methylamine, respectively, between
components of the complex/protein via a biotinyl or
lipoyl group, which is covalently attached to a highly
conserved lysine residue.
Length = 73
Score = 43.6 bits (103), Expect = 1e-05
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 916 QVGAPMP------GSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
+ P G+V++ KVGDKV+KG L + AMK V+AP G VK +
Sbjct: 1 TILIPDLAQHLGDGTVVKWLKKVGDKVKKGDVLAEIEAMKATSDVEAPKSGTVKKV 56
>gnl|CDD|233965 TIGR02660, nifV_homocitr, homocitrate synthase NifV. This family
consists of the NifV clade of homocitrate synthases,
most of which are found in operons for nitrogen
fixation. Members are closely homologous to enzymes that
include 2-isopropylmalate synthase, (R)-citramalate
synthase, and homocitrate synthases associated with
other processes. The homocitrate made by this enzyme
becomes a part of the iron-molybdenum cofactor of
nitrogenase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Other, Central intermediary
metabolism, Nitrogen fixation].
Length = 365
Score = 48.4 bits (116), Expect = 1e-05
Identities = 27/97 (27%), Positives = 47/97 (48%), Gaps = 2/97 (2%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
D G+L P + L+ A+R + D+P+ +H H+ G A+ +A AGA V+ V+ +
Sbjct: 163 DTVGILDPFSTYELVRALR-QAVDLPLEMHAHNDLGMATANTLAAVRAGATHVNTTVNGL 221
Query: 530 SGMTSQPSMGAVVASLQGS-DIDTGLDLKDISAYSAY 565
++ V +L+ DTG+D + A S
Sbjct: 222 GERAGNAALEEVAMALKRLLGRDTGIDTSRLPALSQL 258
>gnl|CDD|132261 TIGR03217, 4OH_2_O_val_ald, 4-hydroxy-2-oxovalerate aldolase.
Members of this protein family are
4-hydroxy-2-oxovalerate aldolase, also called
4-hydroxy-2-ketovalerate aldolase and
2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of
the pathway for the meta-cleavage of catechol, produces
pyruvate and acetaldehyde. Acetaldehyde is then
converted by acetaldehyde dehydrogenase (acylating)
(DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are
tightly associated [Energy metabolism, Other].
Length = 333
Score = 48.1 bits (115), Expect = 1e-05
Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 1/88 (1%)
Query: 470 DMAGLLKPRAAKLLIGAIREK-HPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDS 528
D AG + P + + A++ P+ + H H VA+ IA EAGA +D ++
Sbjct: 164 DSAGAMLPDDVRDRVRALKAVLKPETQVGFHAHHNLSLAVANSIAAIEAGATRIDASLRG 223
Query: 529 MSGMTSQPSMGAVVASLQGSDIDTGLDL 556
+ + VA L +TG DL
Sbjct: 224 LGAGAGNAPLEVFVAVLDRLGWNTGCDL 251
>gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase
A/UDP-N-acetylmuramate--L-alanine ligase; Provisional.
Length = 809
Score = 48.3 bits (115), Expect = 2e-05
Identities = 50/206 (24%), Positives = 85/206 (41%), Gaps = 24/206 (11%)
Query: 66 FIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLK-----YGLPVI 120
+ GPS DKV ++ A D GVP+VP P + + E CL + P+
Sbjct: 555 YTGPSLAFSAIAMDKVLTKRFASDVGVPVVPYQPLTLAGWKREPELCLAHIVEAFSFPMF 614
Query: 121 FKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGD 180
K A+ G G+ V E + SE A + +F+E+ R IEV LGD
Sbjct: 615 VKTAHLGSSIGVFEVHN----VEELRDKISE--AFLYDTDVFVEESRLGSREIEVSCLGD 668
Query: 181 KAGN--VVHLYERDC------SVQRRH----QKVVEIAPAPHLDINVRNKMTDLAVKLAK 228
+ + +ER Q ++ + +I L + ++ +LA ++ +
Sbjct: 669 GSSAYVIAGPHER-RGSGGFIDYQEKYGLSGKSSAQIVFDLDLSKESQEQVLELAERIYR 727
Query: 229 HVGYSNAGTVEFLCDESGQFYFIEVN 254
+ + ++F DE G F+ E+N
Sbjct: 728 LLQGKGSCRIDFFLDEEGNFWLSEMN 753
>gnl|CDD|181282 PRK08195, PRK08195, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic
acid aldolase,; Validated.
Length = 337
Score = 46.7 bits (112), Expect = 4e-05
Identities = 28/91 (30%), Positives = 44/91 (48%), Gaps = 1/91 (1%)
Query: 470 DMAGLLKPRAAKLLIGAIREK-HPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDS 528
D AG L P + + A+R PD + H H+ G GVA+ +A EAGA +D ++
Sbjct: 165 DSAGALLPEDVRDRVRALRAALKPDTQVGFHGHNNLGLGVANSLAAVEAGATRIDGSLAG 224
Query: 529 MSGMTSQPSMGAVVASLQGSDIDTGLDLKDI 559
+ + +VA L +TG+DL +
Sbjct: 225 LGAGAGNTPLEVLVAVLDRMGWETGVDLYKL 255
>gnl|CDD|233366 TIGR01348, PDHac_trf_long, pyruvate dehydrogenase complex
dihydrolipoamide acetyltransferase, long form. This
model describes a subset of pyruvate dehydrogenase
complex dihydrolipoamide acetyltransferase specifically
close by both phylogenetic and per cent identity (UPGMA)
trees. Members of this set include two or three copies
of the lipoyl-binding domain. E. coli AceF is a member
of this model, while mitochondrial and some other
bacterial forms belong to a separate model [Energy
metabolism, Pyruvate dehydrogenase].
Length = 546
Score = 46.4 bits (110), Expect = 7e-05
Identities = 20/53 (37%), Positives = 30/53 (56%)
Query: 917 VGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSIDASM 969
+G G V+E+ VK GDKVE G +L+ L + K M V + G++K I +
Sbjct: 8 IGDNEEGEVIEVLVKPGDKVEAGQSLITLESDKASMEVPSSAAGIIKEIKVKV 60
Score = 44.5 bits (105), Expect = 3e-04
Identities = 26/73 (35%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 899 PDNEMHIHPKAAKSVPGQ------VGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEM 952
P + P A +S Q +G +V+E+ VKVGD V +L+ L + K M
Sbjct: 100 PAAQAQAAPAAGQSSGVQEVTVPDIGDIEKVTVIEVLVKVGDTVSADQSLITLESDKASM 159
Query: 953 VVQAPVQGVVKSI 965
V AP GVVKS+
Sbjct: 160 EVPAPASGVVKSV 172
Score = 31.4 bits (71), Expect = 3.4
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 908 KAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLS 946
KA+ VP AP G V ++VKVGD V G ++ LS
Sbjct: 156 KASMEVP----APASGVVKSVKVKVGDSVPTGDLILTLS 190
Score = 30.2 bits (68), Expect = 6.2
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 908 KAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVL 945
KA+ VP + G + EI+VKVGD + G + L
Sbjct: 40 KASMEVP----SSAAGIIKEIKVKVGDTLPVGGVIATL 73
>gnl|CDD|163678 cd07940, DRE_TIM_IPMS, 2-isopropylmalate synthase (IPMS),
N-terminal catalytic TIM barrel domain.
2-isopropylmalate synthase (IPMS) catalyzes an
aldol-type condensation of acetyl-CoA and
2-oxoisovalerate yielding 2-isopropylmalate and CoA, the
first committed step in leucine biosynthesis. This
family includes the Arabidopsis thaliana IPMS1 and IPMS2
proteins, the Glycine max GmN56 protein, and the
Brassica insularis BatIMS protein. This family also
includes a group of archeal IPMS-like proteins
represented by the Methanocaldococcus jannaschii AksA
protein. AksA catalyzes the condensation of
alpha-ketoglutarate and acetyl-CoA to form
trans-homoaconitate, one of 13 steps in the conversion
of alpha-ketoglutarate and acetylCoA to
alpha-ketosuberate, a precursor to coenzyme B and
biotin. AksA also catalyzes the condensation of
alpha-ketoadipate or alpha-ketopimelate with acetylCoA
to form, respectively, the (R)-homocitrate homologs
(R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and
(R)-2-hydroxy-1,2,6- hexanetricarboxylic acid. This
family belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 268
Score = 45.1 bits (108), Expect = 1e-04
Identities = 30/107 (28%), Positives = 52/107 (48%), Gaps = 12/107 (11%)
Query: 466 INTFDMAGLLKPRAAKLLIGAIRE--KHPDIPIHIHTHDTSGAGVASMIACAEAGADVVD 523
IN D G L P LI ++E + +PI +H H+ G VA+ +A EAGA V+
Sbjct: 160 INIPDTVGYLTPEEFGELIKKLKENVPNIKVPISVHCHNDLGLAVANSLAAVEAGARQVE 219
Query: 524 VAVDSM---SGMTSQPSMGAVVASL----QGSDIDTGLDLKDISAYS 563
++ + +G ++ VV +L ++TG+D +++ S
Sbjct: 220 CTINGIGERAGNA---ALEEVVMALKTRYDYYGVETGIDTEELYETS 263
>gnl|CDD|236999 PRK11854, aceF, pyruvate dehydrogenase dihydrolipoyltransacetylase;
Validated.
Length = 633
Score = 45.0 bits (107), Expect = 2e-04
Identities = 21/43 (48%), Positives = 25/43 (58%)
Query: 923 GSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
V EI VKVGDKVE +L+ + K M V +P GVVK I
Sbjct: 15 VEVTEILVKVGDKVEAEQSLITVEGDKASMEVPSPQAGVVKEI 57
Score = 44.6 bits (106), Expect = 3e-04
Identities = 20/43 (46%), Positives = 23/43 (53%)
Query: 923 GSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
V EI VKVGD VE +L+ + K M V AP G VK I
Sbjct: 118 VEVTEILVKVGDTVEAEQSLITVEGDKASMEVPAPFAGTVKEI 160
Score = 44.2 bits (105), Expect = 3e-04
Identities = 20/46 (43%), Positives = 25/46 (54%)
Query: 923 GSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSIDAS 968
V E+ VKVGDKVE +L+ + K M V AP G VK I +
Sbjct: 219 VEVTEVMVKVGDKVEAEQSLITVEGDKASMEVPAPFAGTVKEIKVN 264
Score = 37.7 bits (88), Expect = 0.038
Identities = 28/77 (36%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 908 KAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSIDA 967
KA+ VP +P G V EI+VKVGDKVE GA +++ + AP Q K A
Sbjct: 41 KASMEVP----SPQAGVVKEIKVKVGDKVETGALIMIFES-ADGAADAAPAQAEEKKEAA 95
Query: 968 SMLLRGANAVGYTNYPD 984
A A + PD
Sbjct: 96 PAAAPAAAAAKDVHVPD 112
Score = 33.8 bits (78), Expect = 0.58
Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 9/52 (17%)
Query: 908 KAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQ 959
KA+ VP AP G+V EI+V VGDKV+ G+ + M+ E+ AP
Sbjct: 245 KASMEVP----APFAGTVKEIKVNVGDKVKTGSLI-----MRFEVEGAAPAA 287
Score = 33.8 bits (78), Expect = 0.64
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 4/38 (10%)
Query: 908 KAAKSVPGQVGAPMPGSVMEIRVKVGDKVEKGAALVVL 945
KA+ VP AP G+V EI+V VGDKV G+ ++V
Sbjct: 144 KASMEVP----APFAGTVKEIKVNVGDKVSTGSLIMVF 177
>gnl|CDD|133458 cd06849, lipoyl_domain, Lipoyl domain of the dihydrolipoyl
acyltransferase component (E2) of 2-oxo acid
dehydrogenases. 2-oxo acid dehydrogenase multienzyme
complexes, like pyruvate dehydrogenase (PDH),
2-oxoglutarate dehydrogenase (OGDH) and branched-chain
2-oxo acid dehydrogenase (BCDH), contain at least three
different enzymes, 2-oxo acid dehydrogenase (E1),
dihydrolipoyl acyltransferase (E2) and dihydrolipoamide
dehydrogenase (E3) and play a key role in redox
regulation. E2, the central component of the complex,
catalyzes the transfer of the acyl group of CoA from E1
to E3 via reductive acetylation of a lipoyl group
covalently attached to a lysine residue.
Length = 74
Score = 40.1 bits (95), Expect = 2e-04
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 923 GSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
G+++E VK GD VE+G L + K + V+AP GV+ I
Sbjct: 15 GTIVEWLVKEGDSVEEGDVLAEVETDKATVEVEAPAAGVLAKI 57
Score = 30.8 bits (71), Expect = 0.51
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 919 APMPGSVMEIRVKVGDKVEKGAALVVL 945
AP G + +I V+ GD V G + V+
Sbjct: 48 APAAGVLAKILVEEGDTVPVGQVIAVI 74
>gnl|CDD|163677 cd07939, DRE_TIM_NifV, Streptomyces rubellomurinus FrbC and related
proteins, catalytic TIM barrel domain. FrbC (NifV) of
Streptomyces rubellomurinus catalyzes the condensation
of acetyl-CoA and alpha-ketoglutarate to form
homocitrate and CoA, a reaction similar to one catalyzed
by homocitrate synthase. The gene encoding FrbC is one
of several genes required for the biosynthesis of
FR900098, a potent antimalarial antibiotic. This
protein is also required for assembly of the nitrogenase
MoFe complex but its exact role is unknown. This
family also includes the NifV proteins of Heliobacterium
chlorum and Gluconacetobacter diazotrophicus, which
appear to be orthologous to FrbC. This family belongs
to the DRE-TIM metallolyase superfamily. DRE-TIM
metallolyases include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 259
Score = 43.6 bits (104), Expect = 3e-04
Identities = 29/100 (29%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
D G+L P LI +R D+P+ H H+ G A+ +A AGA V V V+ +
Sbjct: 160 DTVGILDPFTTYELIRRLR-AATDLPLEFHAHNDLGLATANTLAAVRAGATHVSVTVNGL 218
Query: 530 ---SGMTSQPSMGAVVASLQGS-DIDTGLDLKDISAYSAY 565
+G ++ VV +L+ DTG+D + S
Sbjct: 219 GERAGN---AALEEVVMALKHLYGRDTGIDTTRLPELSQL 255
>gnl|CDD|180605 PRK06524, PRK06524, biotin carboxylase-like protein; Validated.
Length = 493
Score = 44.3 bits (105), Expect = 3e-04
Identities = 48/237 (20%), Positives = 82/237 (34%), Gaps = 53/237 (22%)
Query: 61 DAGIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGL--P 118
AG+ + P + ++ K+ + A ++GVP VP G + + +E GL
Sbjct: 124 QAGLEVMHPPAELRHRLDSKIVTTRLANEAGVPSVPHVLGRVDSYDELSALAHGAGLGDD 183
Query: 119 VIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLL 178
++ + YG G VR D ++ + + K ++R R++EV +
Sbjct: 184 LVVQTPYGDSGSTTFFVRGQRDWDKYAGGIVGQPEI----------KVMKRIRNVEVCIE 233
Query: 179 GDKAGNVVHLYERDCSVQRRHQKVV-----EIAPAPHL----------DI-------NVR 216
RH V+ + P L DI
Sbjct: 234 A---------------CVTRHGTVIGPAMTSLVGYPELTPYRGGWCGNDIWPGALPPAQT 278
Query: 217 NKMTDLAVKLAKHV---GYSNAGTVEFLCD-ESGQFYFIEVNARLQVEHTVTEEITG 269
K ++ KL + GY V+ L D ++ + Y EVN RL +T T
Sbjct: 279 RKAREMVRKLGDVLSREGYRGYFEVDLLHDLDADELYLGEVNPRLSGASPMTNLTTE 335
>gnl|CDD|180206 PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyase; Provisional.
Length = 287
Score = 43.3 bits (103), Expect = 4e-04
Identities = 33/121 (27%), Positives = 51/121 (42%), Gaps = 16/121 (13%)
Query: 459 EIPLGKLINTFDMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAG 518
EI LG D G+ P + ++ A+ + P + H HDT G +A++ A E G
Sbjct: 171 EISLG------DTIGVGTPGQVRAVLEAVLAEFPAERLAGHFHDTYGQALANIYASLEEG 224
Query: 519 ADVVDVAVDSMSGMTSQPSMGA--------VVASLQGSDIDTGLDLKDISAYSAYWEQTR 570
V D +V + G P GA V+ L G I+TG+DL + + +
Sbjct: 225 ITVFDASVGGLGGCPYAP--GASGNVATEDVLYMLHGLGIETGIDLDKLVRAGQFIQSKL 282
Query: 571 Q 571
Sbjct: 283 G 283
>gnl|CDD|235777 PRK06302, PRK06302, acetyl-CoA carboxylase biotin carboxyl carrier
protein subunit; Validated.
Length = 155
Score = 41.3 bits (98), Expect = 5e-04
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 930 VKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
V+VGD V++G L ++ AMK+ ++A GVV I
Sbjct: 102 VEVGDTVKEGQTLCIIEAMKVMNEIEADKSGVVTEI 137
>gnl|CDD|235010 PRK02186, PRK02186, argininosuccinate lyase; Provisional.
Length = 887
Score = 43.7 bits (103), Expect = 6e-04
Identities = 64/296 (21%), Positives = 106/296 (35%), Gaps = 44/296 (14%)
Query: 33 VAKENDVDAIHPGYGFLSERSDFAQAVLDAGIRFIGPSPYVVQQMG-------------D 79
A +D D IH F+S A ++ + FI + V +++G D
Sbjct: 52 SADTSDPDRIH---RFVSSLDGVA-GIMSSSEYFIEVASEVARRLGLPAANTEAIRTCRD 107
Query: 80 KVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKME 139
K + D G+ VP T + A++ PV+ K G G G+R+ +
Sbjct: 108 KKRLARTLRDHGID-VPRTHA-LALRAVALDALDGLTYPVVVKPRMGSGSVGVRLCASVA 165
Query: 140 DVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVVHLYERDCSVQRRH 199
+ + G A ++ ++E + V+ L G+ V + R+H
Sbjct: 166 EAAAHCAALRRA-----GTRAALVQAYVEGDEY-SVETLTVARGHQV------LGITRKH 213
Query: 200 Q----KVVEIA---PAPHLDINVRNKMTDLAVKLAKHVGYS-NAGTVEFLCDESGQFYFI 251
VEI PAP L R ++ ++ VGY+ E I
Sbjct: 214 LGPPPHFVEIGHDFPAP-LSAPQRERIVRTVLRALDAVGYAFGPAHTELRVRGDT-VVII 271
Query: 252 EVNARLQ--VEHTVTEEITGVDLVQSQIRVAEGMTLPELGLTQEKISPQGFAIQCR 305
E+N RL + + EE GVDL+ I + G T ++ F + R
Sbjct: 272 EINPRLAGGMIPVLLEEAFGVDLLDHVIDLHLG-VAAFADPTAKRYGAIRFVLPAR 326
>gnl|CDD|233719 TIGR02090, LEU1_arch, isopropylmalate/citramalate/homocitrate
synthases. Methanogenic archaea contain three closely
related homologs of the 2-isopropylmalate synthases
(LeuA) represented by TIGR00973. Two of these in
Methanococcus janaschii (MJ1392 - CimA ; MJ0503 - AksA )
have been characterized as catalyzing alternative
reactions leaving the third (MJ1195) as the presumptive
LeuA enzyme. CimA is citramalate (2-methylmalate)
synthase which condenses acetyl-CoA with pyruvate. This
enzyme is believed to be involved in the biosynthesis of
isoleucine in methanogens and possibly other species
lacking threonine dehydratase. AksA is a homocitrate
synthase which also produces (homo)2-citrate and
(homo)3-citrate in the biosynthesis of Coenzyme B which
is restricted solely to methanogenic archaea.
Methanogens, then should and aparrently do contain all
three of these enzymes. Unfortunately, phylogenetic
trees do not resolve into three unambiguous clades,
making assignment of function to particular genes
problematic. Other archaea which lack a threonine
dehydratase (mainly Euryarchaeota) should contain both a
CimA and a LeuA gene. This is true of, for example,
archaeoglobus fulgidis, but not for the Pyrococci which
have none in this clade, but one in TIGR00973 and one in
TIGRT00977 which may fulfill these roles. Other species
which have only one hit to this model and lack threonine
dehydratase are very likely LeuA enzymes.
Length = 363
Score = 42.9 bits (101), Expect = 7e-04
Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 2/92 (2%)
Query: 466 INTFDMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVA 525
IN D G+L P+ + LI ++E +PI +H H+ G A+ IA +AGA+ V V
Sbjct: 158 INIADTVGVLTPQKMEELIKKLKEN-VKLPISVHCHNDFGLATANSIAGVKAGAEQVHVT 216
Query: 526 VDSMSGMTSQPSMGAVVASLQG-SDIDTGLDL 556
V+ + ++ VV +L+ + T +
Sbjct: 217 VNGIGERAGNAALEEVVMALKYLYGVKTKIKT 248
>gnl|CDD|163683 cd07945, DRE_TIM_CMS, Leptospira interrogans citramalate synthase
(CMS) and related proteins, N-terminal catalytic TIM
barrel domain. Citramalate synthase (CMS) catalyzes the
conversion of pyruvate and acetyl-CoA to (R)-citramalate
in the first dedicated step of the citramalate pathway.
Citramalate is only found in Leptospira interrogans and
a few other microorganisms. This family belongs to the
DRE-TIM metallolyase superfamily. DRE-TIM metallolyases
include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 280
Score = 42.4 bits (100), Expect = 7e-04
Identities = 21/95 (22%), Positives = 44/95 (46%), Gaps = 1/95 (1%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
D G+L P I + +++P++ H H+ VA+++A +AG + V+ +
Sbjct: 168 DTLGILSPFETYTYISDMVKRYPNLHFDFHAHNDYDLAVANVLAAVKAGIKGLHTTVNGL 227
Query: 530 SGMTSQPSMGAVVASLQG-SDIDTGLDLKDISAYS 563
+ +V+A L+ + T +D K ++ S
Sbjct: 228 GERAGNAPLASVIAVLKDKLKVKTNIDEKRLNRAS 262
>gnl|CDD|236493 PRK09389, PRK09389, (R)-citramalate synthase; Provisional.
Length = 488
Score = 43.0 bits (102), Expect = 8e-04
Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 2/91 (2%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
D G+L P L + E P+ IH H+ G VA+ +A AGAD V V ++ +
Sbjct: 164 DTVGILTPEKTYELFKRLSEL-VKGPVSIHCHNDFGLAVANTLAALAAGADQVHVTINGI 222
Query: 530 SGMTSQPSMGAVVASL-QGSDIDTGLDLKDI 559
S+ VV +L D++TG+ L+++
Sbjct: 223 GERAGNASLEEVVMALKHLYDVETGIKLEEL 253
>gnl|CDD|163679 cd07941, DRE_TIM_LeuA3, Desulfobacterium autotrophicum LeuA3 and
related proteins, N-terminal catalytic TIM barrel
domain. Desulfobacterium autotrophicum LeuA3 is
sequence-similar to alpha-isopropylmalate synthase
(LeuA) but its exact function is unknown. Members of
this family have an N-terminal TIM barrel domain that
belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 273
Score = 41.7 bits (99), Expect = 0.001
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 484 IGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVV 522
+ +RE+ P +P+ IH H+ SG VA+ +A EAGA V
Sbjct: 186 VKEVRERLPGVPLGIHAHNDSGLAVANSLAAVEAGATQV 224
>gnl|CDD|168348 PRK06015, PRK06015,
keto-hydroxyglutarate-aldolase/keto-deoxy-
phosphogluconate aldolase; Provisional.
Length = 201
Score = 41.0 bits (96), Expect = 0.001
Identities = 41/122 (33%), Positives = 50/122 (40%), Gaps = 21/122 (17%)
Query: 13 LVGKGLPPVEAYLNIPE----IIRVAKENDVDAIHPGYGFLSERSDFAQAVLDAGIRFIG 68
L GLP +E L P I VA E V+ G G + F A AG RFI
Sbjct: 25 LAAGGLPAIEITLRTPAALDAIRAVAAE--VEEAIVGAGTILNAKQFEDAA-KAGSRFI- 80
Query: 69 PSPYVVQQMGDKVAARQAAIDSGVPIVPG--TPGPITTTEEAMEFCLKYGLPVIFKAAYG 126
SP Q++ AA DS VP++PG TP + E LK+ F A
Sbjct: 81 VSPGTTQELLA------AANDSDVPLLPGAATPSEVMALREEGYTVLKF-----FPAEQA 129
Query: 127 GG 128
GG
Sbjct: 130 GG 131
>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed.
Length = 547
Score = 41.7 bits (99), Expect = 0.002
Identities = 19/43 (44%), Positives = 26/43 (60%)
Query: 923 GSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
V+E VKVGD VE+ +L+ + K M + +PV GVVK I
Sbjct: 133 VEVIEWLVKVGDTVEEDQSLITVETDKATMEIPSPVAGVVKEI 175
Score = 37.9 bits (89), Expect = 0.029
Identities = 18/43 (41%), Positives = 23/43 (53%)
Query: 923 GSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
V+E VK GD VE+ LV + K M + +P GVVK I
Sbjct: 16 VEVIEWLVKEGDTVEEDQPLVTVETDKATMEIPSPAAGVVKEI 58
Score = 34.4 bits (80), Expect = 0.33
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 916 QVGAPMPGSVMEIRVKVGDKVEKGAALVVL 945
++ +P G V EI+VKVGD V G L V+
Sbjct: 46 EIPSPAAGVVKEIKVKVGDTVSVGGLLAVI 75
Score = 34.4 bits (80), Expect = 0.38
Identities = 16/30 (53%), Positives = 23/30 (76%)
Query: 916 QVGAPMPGSVMEIRVKVGDKVEKGAALVVL 945
++ +P+ G V EI+VKVGDKV G+ LVV+
Sbjct: 163 EIPSPVAGVVKEIKVKVGDKVSVGSLLVVI 192
>gnl|CDD|223229 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide
transport and metabolism].
Length = 428
Score = 41.0 bits (97), Expect = 0.003
Identities = 43/165 (26%), Positives = 65/165 (39%), Gaps = 16/165 (9%)
Query: 8 ADESYLVGKGLPPVEAYLNIPEIIRVAKENDVDAIHPG-YGFLSERSDFAQAVLDAGIRF 66
A E+YLV + + ++ AKE +VD + G L A+ AGI
Sbjct: 38 ALEAYLVNIEID-----TDHEALVAFAKEKNVDLVVVGPEAPLVA--GVVDALRAAGIPV 90
Query: 67 IGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYG 126
GP+ Q G K A+ G+P T EEA + + G P++ KA
Sbjct: 91 FGPTKAAAQLEGSKAFAKDFMKKYGIPT--AEYEVFTDPEEAKAYIDEKGAPIVVKADGL 148
Query: 127 GGGRGMRVVRKMEDVEENFQRASSE-AKAAFGNGAMF--IEKFIE 168
G+G+ V +EE AFG+ IE+F++
Sbjct: 149 AAGKGVIVA---MTLEEAEAAVDEMLEGNAFGSAGARVVIEEFLD 190
>gnl|CDD|223106 COG0027, PurT, Formate-dependent phosphoribosylglycinamide
formyltransferase (GAR transformylase) [Nucleotide
transport and metabolism].
Length = 394
Score = 40.8 bits (96), Expect = 0.003
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 103 TTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMF 162
+ EE K G P + K G+G VVR EDVE+ ++ A + G+G +
Sbjct: 136 DSLEELRAAVEKIGFPCVVKPVMSSSGKGQSVVRSPEDVEKAWEYAQQGGRG--GSGRVI 193
Query: 163 IEKFIE 168
+E+F++
Sbjct: 194 VEEFVK 199
>gnl|CDD|217166 pfam02655, ATP-grasp_3, ATP-grasp domain. No functional
information or experimental verification of function is
known in this family. This family appears to be an
ATP-grasp domain (Pers. obs. A Bateman).
Length = 159
Score = 38.5 bits (90), Expect = 0.005
Identities = 43/193 (22%), Positives = 72/193 (37%), Gaps = 48/193 (24%)
Query: 78 GDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRK 137
DK+ +A ++GVP+ P T + E K I K G GG G VR
Sbjct: 1 SDKLKTYKALKNAGVPV------PTTLSAEEPTEEEK---KYIVKPRDGCGGEG---VRF 48
Query: 138 MEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVVHLYERDCSVQR 197
+E+ E+ + I++FIE + V +L D SV R
Sbjct: 49 VENGREDE----------EFIENVIIQEFIE-GEPLSVSVLSDGEKV------LPLSVNR 91
Query: 198 RHQKVVE--------IAPAPHLDINVRNKMTDLAVKLAKH----VGYSNAGTVEFLCDES 245
+ + P+ ++ ++ +LA ++ + GY V+ + +
Sbjct: 92 QLIDNAGSGFVYAGNVTPSRT---ELKEELEELAEEVVEALPGLNGYVG---VDLVLTDG 145
Query: 246 GQFYFIEVNARLQ 258
G Y IEVN R+
Sbjct: 146 GP-YVIEVNPRIT 157
>gnl|CDD|130046 TIGR00973, leuA_bact, 2-isopropylmalate synthase, bacterial type.
This is the first enzyme of leucine biosynthesis. A
larger family of homologous proteins includes
homocitrate synthase, distinct lineages of
2-isopropylmalate synthase, several distinct,
uncharacterized, orthologous sets in the Archaea, and
other related enzymes. This model describes a family of
2-isopropylmalate synthases found primarily in Bacteria.
The homologous families in the Archaea may represent
isozymes and/or related enzymes [Amino acid
biosynthesis, Pyruvate family].
Length = 494
Score = 40.1 bits (94), Expect = 0.006
Identities = 28/105 (26%), Positives = 49/105 (46%), Gaps = 7/105 (6%)
Query: 466 INTFDMAGLLKPRAAKLLIGAIREKHPDIP---IHIHTHDTSGAGVASMIACAEAGADVV 522
IN D G P LI +RE P+I + +H H+ G VA+ +A + GA V
Sbjct: 163 INIPDTVGYALPAEYGNLIKGLRENVPNIDKAILSVHCHNDLGLAVANSLAAVQNGARQV 222
Query: 523 DVAVDSMSGMTSQPSMGAVVASLQGS----DIDTGLDLKDISAYS 563
+ ++ + ++ VV +L+ ++TG++ K+I S
Sbjct: 223 ECTINGIGERAGNAALEEVVMALKVRKDFLGVETGINTKEIYRTS 267
>gnl|CDD|234993 PRK01966, ddl, D-alanyl-alanine synthetase A; Reviewed.
Length = 333
Score = 39.7 bits (94), Expect = 0.006
Identities = 50/221 (22%), Positives = 82/221 (37%), Gaps = 45/221 (20%)
Query: 57 QAVLD-AGIRFIGPSPYV-VQQMGDKVAARQAAIDSGVPIVP------GTPGPITTTEEA 108
Q +L+ GI ++G M DK+ ++ +G+P+ P G + E
Sbjct: 100 QGLLELLGIPYVGCGVLASALSM-DKILTKRLLAAAGIPVAPYVVLTRGDWEEASLAEIE 158
Query: 109 MEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIE 168
+ GLPV K A G G+ V+ E++ A + +E+ I+
Sbjct: 159 AKL----GLPVFVKPANLGSSVGISKVKNEEELAAALDLAFEYDRKV------LVEQGIK 208
Query: 169 RPRHIEVQLLGDKAGNVVHLYERDCS----VQRRH-----------QKVVEIAPAPHLDI 213
R IE +LG + S + + I PA L
Sbjct: 209 -GREIECAVLG---------NDPKASVPGEIVKPDDFYDYEAKYLDGSAELIIPAD-LSE 257
Query: 214 NVRNKMTDLAVKLAKHVGYSNAGTVEFLCDESGQFYFIEVN 254
+ K+ +LA+K K +G S V+F E G+ Y E+N
Sbjct: 258 ELTEKIRELAIKAFKALGCSGLARVDFFLTEDGEIYLNEIN 298
>gnl|CDD|233705 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin is
an insoluble storage polymer for carbon, nitrogen, and
energy, found in most Cyanobacteria. The polymer has a
backbone of L-aspartic acid, with most Asp side chain
carboxyl groups attached to L-arginine. The polymer is
made by this enzyme, cyanophycin synthetase, and
degraded by cyanophycinase. Heterologously expressed
cyanophycin synthetase in E. coli produces a closely
related, water-soluble polymer with some Arg replaced by
Lys. It is unclear whether enzymes that produce soluble
cyanophycin-like polymers in vivo in non-Cyanobacterial
species should be designated as cyanophycin synthetase
itself or as a related enzyme. This model makes the
designation as cyanophycin synthetase. Cyanophycin
synthesis is analogous to polyhydroxyalkanoic acid (PHA)
biosynthesis, except that PHA polymers lack nitrogen and
may be made under nitrogen-limiting conditions [Cellular
processes, Biosynthesis of natural products].
Length = 864
Score = 40.1 bits (94), Expect = 0.007
Identities = 32/115 (27%), Positives = 56/115 (48%), Gaps = 13/115 (11%)
Query: 79 DKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRV-VRK 137
DK ++ D+GVP+ GT + + E+A E G PV+ K G GRG+ + +
Sbjct: 213 DKDLTKEILSDAGVPVPEGTV--VQSAEDAWEAAQDLGYPVVIKPYDGNHGRGVTINILT 270
Query: 138 MEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVVHLYERD 192
+++E ++ A E+ + +E+FI R + ++G K VV + ER
Sbjct: 271 RDEIESAYEAAVEESS------GVIVERFI-TGRDHRLLVVGGK---VVAVAERV 315
>gnl|CDD|188060 TIGR00531, BCCP, acetyl-CoA carboxylase, biotin carboxyl carrier
protein. This model is designed to identify biotin
carboxyl carrier protein as a peptide of acetyl-CoA
carboxylase. Scoring below the trusted cutoff is a
related protein encoded in a region associated with
polyketide synthesis in the prokaryote Saccharopolyspora
hirsuta, and a reported chloroplast-encoded biotin
carboxyl carrier protein that may be highly derived from
the last common ancestral sequence. Scoring below the
noise cutoff are biotin carboxyl carrier domains of
other enzymes such as pyruvate carboxylase.The gene name
is accB or fabE [Fatty acid and phospholipid metabolism,
Biosynthesis].
Length = 156
Score = 38.3 bits (89), Expect = 0.007
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 919 APMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSIDASMLLRGANAVG 978
AP P + + V+VGDKV+KG + ++ AMK+ ++A V G V I L+ V
Sbjct: 94 APSPDA--KPFVEVGDKVKKGQIVCIVEAMKLMNEIEAEVAGKVVEI----LVENGQPVE 147
Query: 979 Y 979
Y
Sbjct: 148 Y 148
>gnl|CDD|130212 TIGR01142, purT, phosphoribosylglycinamide formyltransferase 2.
This enzyme is an alternative to PurN (TIGR00639)
[Purines, pyrimidines, nucleosides, and nucleotides,
Purine ribonucleotide biosynthesis].
Length = 380
Score = 39.7 bits (93), Expect = 0.008
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 103 TTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMF 162
+ +E E K G P + K G+G VVR ED+E+ ++ A A+ G G +
Sbjct: 123 DSLDELREAVEKIGYPCVVKPVMSSSGKGQSVVRGPEDIEKAWEYAQEGARG--GAGRVI 180
Query: 163 IEKFIE 168
+E+FI+
Sbjct: 181 VEEFID 186
>gnl|CDD|223582 COG0508, AceF, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide acyltransferase (E2) component, and
related enzymes [Energy production and conversion].
Length = 404
Score = 39.7 bits (93), Expect = 0.008
Identities = 19/43 (44%), Positives = 26/43 (60%)
Query: 923 GSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
G+++E KVGDKV++G LV + K M V AP GV+ I
Sbjct: 17 GTIVEWLKKVGDKVKEGDVLVEVETDKATMEVPAPDAGVLAKI 59
>gnl|CDD|223267 COG0189, RimK, Glutathione synthase/Ribosomal protein S6
modification enzyme (glutaminyl transferase) [Coenzyme
metabolism / Translation, ribosomal structure and
biogenesis].
Length = 318
Score = 39.3 bits (92), Expect = 0.008
Identities = 49/243 (20%), Positives = 85/243 (34%), Gaps = 46/243 (18%)
Query: 32 RVAKENDVDAIHPGYG-FLSERSDFAQAVLDAGIRFIGPSPYVVQQMGDKVAARQAAIDS 90
++ +++D I + F + G+ I P +++ +K+ Q +
Sbjct: 72 DLSLLDELDVIIMRKDPPFDFATRFLRLAERKGVPVI-NDPQSIRRCRNKLYTTQLLAKA 130
Query: 91 GVPIVPGT------PGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEEN 144
G+P VP T E + F PV+ K G GGRG V +ED +
Sbjct: 131 GIP-VPPTLITRDPDEAAEFVAEHLGF------PVVLKPLDGSGGRG---VFLVEDADPE 180
Query: 145 FQRASSEAKAAFGNGAMFIEKFIERPRH-IEVQLLGDKAGNVVHLYERDCSVQRRHQK-- 201
G + ++++I + + L+G VV +Y ++ R
Sbjct: 181 LLSLLETLT-QEGRKLIIVQEYIPKAKRDDRRVLVGGGE--VVAIY----ALARIPASGD 233
Query: 202 ---------VVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLCDESGQFYFIE 252
E + +LAVK A +G G V+ + D+ G Y E
Sbjct: 234 FRSNLARGGRAEPCELT-------EEEEELAVKAAPALGLGLVG-VDIIEDKDG-LYVTE 284
Query: 253 VNA 255
VN
Sbjct: 285 VNV 287
>gnl|CDD|162241 TIGR01182, eda, Entner-Doudoroff aldolase.
2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14)
is an enzyme of the Entner-Doudoroff pathway. This
aldolase has another function, 4-hydroxy-2-oxoglutarate
aldolase (EC 4.1.3.16) shown experimentally in
Escherichia coli and Pseudomonas putida [Amino acid
biosynthesis, Glutamate family, Energy metabolism,
Entner-Doudoroff].
Length = 204
Score = 38.4 bits (90), Expect = 0.009
Identities = 34/107 (31%), Positives = 49/107 (45%), Gaps = 23/107 (21%)
Query: 13 LVGKGLPPVEAYLNIP---EIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDAGIRFI-- 67
L+ GL +E L P + IR+ ++ DA+ G G + QAV DAG +FI
Sbjct: 29 LIEGGLRVLEVTLRTPVALDAIRLLRKEVPDAL-IGAGTVLNPEQLRQAV-DAGAQFIVS 86
Query: 68 -GPSPYVVQQMGDKVAARQAAIDSGVPIVPG--TPGPITTTEEAMEF 111
G +P + + A D G+PI+PG TP I A+E
Sbjct: 87 PGLTPELAK----------HAQDHGIPIIPGVATPSEI---MLALEL 120
>gnl|CDD|184327 PRK13789, PRK13789, phosphoribosylamine--glycine ligase;
Provisional.
Length = 426
Score = 39.1 bits (91), Expect = 0.010
Identities = 25/114 (21%), Positives = 46/114 (40%), Gaps = 2/114 (1%)
Query: 55 FAQAVLDAGIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLK 114
FA + GI GP Y Q G K A+ ++ +P + T ++ +
Sbjct: 84 FADWAAELGIPCFGPDSYCAQVEGSKHFAKSLMKEAKIPT--ASYKTFTEYSSSLSYLES 141
Query: 115 YGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIE 168
LP++ KA G+G+ V + + + + + K + IE+F+E
Sbjct: 142 EMLPIVIKADGLAAGKGVTVATEKKMAKRALKEIFKDKKFGQSGNQVVIEEFME 195
>gnl|CDD|233164 TIGR00877, purD, phosphoribosylamine--glycine ligase. Alternate
name: glycinamide ribonucleotide synthetase (GARS). This
enzyme appears as a monofunctional protein in
prokaryotes but as part of a larger, multidomain protein
in eukaryotes [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 422
Score = 39.2 bits (92), Expect = 0.011
Identities = 42/178 (23%), Positives = 66/178 (37%), Gaps = 19/178 (10%)
Query: 26 NIPEIIRVAKENDVDAIHPG-YGFLSERSDFAQAVLDAGIRFIGPSPYVVQQMGDKVAAR 84
+I ++ AK+ +D G L A+ +AGI GP+ Q G K A+
Sbjct: 52 DIEALVEFAKKKKIDLAIIGPEAPLVL--GLVDALEEAGIPVFGPTKEAAQLEGSKAFAK 109
Query: 85 QAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEEN 144
G+P T EEA + + G P++ KA G+G+ V + E+ +
Sbjct: 110 DFMKRYGIPTAEYEV--FTDPEEAKSYIQEKGAPIVVKADGLAAGKGVIVAKTNEEAIKA 167
Query: 145 FQRASSEAKAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVV----------HLYERD 192
+ E K + IE+F++ E LL G V E D
Sbjct: 168 VEDI-LEQKFGDAGERVVIEEFLDGE---EFSLLAFVDGKTVIPMPPAQDHKRALEGD 221
>gnl|CDD|163682 cd07944, DRE_TIM_HOA_like, 4-hydroxy-2-oxovalerate aldolase-like,
N-terminal catalytic TIM barrel domain. This family of
bacterial enzymes is sequence-similar to
4-hydroxy-2-oxovalerate aldolase (HOA) but its exact
function is unknown. This family includes the
Bacteroides vulgatus Bvu_2661 protein and belongs to the
DRE-TIM metallolyase superfamily. DRE-TIM metallolyases
include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 266
Score = 38.3 bits (90), Expect = 0.013
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 473 GLLKPRAAKLLIGAIREK-HPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSMSG 531
G + P K +I +R DI + H H+ +A+ + E G +++D ++ G
Sbjct: 162 GSMYPEDIKRIISLLRSNLDKDIKLGFHAHNNLQLALANTLEAIELGVEIIDA---TVYG 218
Query: 532 M 532
M
Sbjct: 219 M 219
>gnl|CDD|213969 TIGR04356, grasp_GAK, ATP-grasp enzyme, GAK system. Members of
this family are ATP-grasp family enzymes related to a
number of characterized glutamate ligases, including the
ribosomal protein S6 modification enzyme RimK. This
group belongs to a conserved gene neighborhood that also
features an HPr kinase-related protein (see TIGR04355).
We assign this system the initial designation GAK, for
Grasp (this ATP-grasp family enzyme), Amphipathic (for
the member of family TIGR04354, designated Amphi-Trp),
and Kinase, for the HPr-kinase homolog TIGR04355.
Length = 287
Score = 38.1 bits (89), Expect = 0.017
Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 21/102 (20%)
Query: 73 VVQQMGDKVAARQAAIDSGVPIVPGTPGPIT-TTEEAMEFCLKYGLPVIFKAAYGGGGRG 131
++ ++ V+ RQ I P P +T + A+E +YG +FK Y RG
Sbjct: 97 LIDRLSCTVSLRQGDI-------PMPPTVVTEDLDAALEAVERYG-KAVFKPLYSTKARG 148
Query: 132 MRVVRKMEDVE---ENFQRASSEAKAAFGNGAMFIEKFIERP 170
M V+ + E F++ GN M+I++ + P
Sbjct: 149 MEVLEPGPGLRAALEAFRQ---------GNPFMYIQQKVNLP 181
>gnl|CDD|205711 pfam13533, Biotin_lipoyl_2, Biotin-lipoyl like.
Length = 50
Score = 34.0 bits (79), Expect = 0.020
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 916 QVGAPMPGSVMEIRVKVGDKVEKGAALVVLS 946
+ P+ G V+ + VK G V+KG L L
Sbjct: 4 NIAPPVSGRVVAVNVKEGQSVKKGDVLFTLD 34
>gnl|CDD|162728 TIGR02146, LysS_fung_arch, homocitrate synthase. This model
includes the yeast LYS21 gene which carries out the
first step of the alpha-aminoadipate (AAA) lysine
biosynthesis pathway. A related pathway is found in
Thermus thermophilus. This enzyme is closely related to
2-isopropylmalate synthase (LeuA) and citramalate
synthase (CimA), both of which are present in the
euryarchaeota. Some archaea have a separate homocitrate
synthase (AksA) which also synthesizes longer
homocitrate analogs.
Length = 344
Score = 38.2 bits (89), Expect = 0.020
Identities = 19/57 (33%), Positives = 26/57 (45%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAV 526
D G PR LI + P + I +H H+ +G VA+ E GA +VD V
Sbjct: 160 DTVGKAAPRQVYELIRTVVRVVPGVDIELHAHNDTGCAVANAYNAIEGGATIVDTTV 216
>gnl|CDD|199870 cd06250, M14_PaAOTO_like, Peptidase M14 Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA)-like
subfamily; subgroup includes Pseudomonas aeruginosa
AotO. An uncharacterized subgroup of the
Succinylglutamate desuccinylase (ASTE)/aspartoacylase
(ASPA) subfamily which is part of the the M14 family of
metallocarboxypeptidases. This subgroup includes
Pseudomonas aeruginosa AotO and related proteins. ASTE
catalyzes the fifth and last step in arginine catabolism
by the arginine succinyltransferase pathway, and
aspartoacylase (ASPA, also known as aminoacylase 2, and
ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid
(NAA) into aspartate and acetate. NAA is abundant in the
brain, and hydrolysis of NAA by ASPA may help maintain
white matter. ASPA is an NAA scavenger in other tissues.
Mutations in the gene encoding ASPA cause Canavan
disease (CD), a fatal progressive neurodegenerative
disorder involving dysmyelination and spongiform
degeneration of white matter in children. This enzyme
binds zinc which is necessary for activity. Measurement
of elevated NAA levels in urine is used in the diagnosis
of CD. The gene encoding P. aeruginosa AotO was
characterized as part of an operon encoding an arginine
and ornithine transport system, however it is not
essential for arginine and ornithine uptake.
Length = 359
Score = 38.0 bits (89), Expect = 0.024
Identities = 35/147 (23%), Positives = 44/147 (29%), Gaps = 41/147 (27%)
Query: 849 ENWGGATFDVALRFLHECPWERLEEMRKQIPNIPFQML-----LRGANAVGYTNYPDNEM 903
+N GG FD A CPW L+E IP LRG V + E
Sbjct: 202 DNSGGGAFDEA----FSCPWWALQERFGDGRPIPVGCEAVTVELRGQEDV---DLALAEK 254
Query: 904 -----------------HIHPKAAKSVPG-------QVGAPMPGSVMEIRVKVGDKVEKG 939
P P + AP G ++ R GD VE G
Sbjct: 255 DAEGILRYLVHRGVIAGDAAPLPPLRRPATPLAGYEMLYAPAGG-LVVYRAAPGDWVEAG 313
Query: 940 AALV-VLSAMKMEMVVQ---APVQGVV 962
L +L + AP GV+
Sbjct: 314 DLLAEILDPLGDGSGTTAVRAPQDGVL 340
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 37.2 bits (87), Expect = 0.030
Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 12/73 (16%)
Query: 86 AAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEENF 145
A+D+ + +V G TE+ EF LP I + KM+ +F
Sbjct: 86 RAVDAALIVVEAQSGVEVGTEKVWEFLDDAKLPRII------------FINKMDRARADF 133
Query: 146 QRASSEAKAAFGN 158
+ + + AFG
Sbjct: 134 DKTLAALREAFGR 146
>gnl|CDD|237586 PRK14016, PRK14016, cyanophycin synthetase; Provisional.
Length = 727
Score = 37.8 bits (89), Expect = 0.035
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 89 DSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRV-VRKMEDVEENFQR 147
+GVP+ G +T+ E+A E + G PV+ K G GRG+ V + E++E +
Sbjct: 224 AAGVPVPEGRV--VTSAEDAWEAAEEIGYPVVVKPLDGNHGRGVTVNITTREEIEAAYAV 281
Query: 148 ASSEAKAAFGNGAMFIEKFIE 168
AS E + + +E++I
Sbjct: 282 ASKE-----SSDVI-VERYIP 296
>gnl|CDD|178347 PLN02746, PLN02746, hydroxymethylglutaryl-CoA lyase.
Length = 347
Score = 37.1 bits (86), Expect = 0.041
Identities = 30/107 (28%), Positives = 47/107 (43%), Gaps = 18/107 (16%)
Query: 459 EIPLGKLINTFDMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAG 518
EI LG D G+ P ++ A+ P + +H HDT G +A+++ + G
Sbjct: 213 EISLG------DTIGVGTPGTVVPMLEAVMAVVPVDKLAVHFHDTYGQALANILVSLQMG 266
Query: 519 ADVVDVAVDSMSGMTSQP-SMGA--------VVASLQGSDIDTGLDL 556
VD S++G+ P + GA VV L G + T +DL
Sbjct: 267 ISTVD---SSVAGLGGCPYAKGASGNVATEDVVYMLNGLGVSTNVDL 310
>gnl|CDD|184849 PRK14847, PRK14847, hypothetical protein; Provisional.
Length = 333
Score = 36.9 bits (85), Expect = 0.042
Identities = 21/79 (26%), Positives = 38/79 (48%)
Query: 494 IPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSMSGMTSQPSMGAVVASLQGSDIDTG 553
I + +H H+ G VA+ AGA+ ++ + T + A+ +L+ I +G
Sbjct: 241 IVLSVHPHNDRGTAVAAAELAVLAGAERIEGCLFGNGERTGNVDLVALALNLERQGIASG 300
Query: 554 LDLKDISAYSAYWEQTRQL 572
LD +D++A A + QL
Sbjct: 301 LDFRDMAALRACVSECNQL 319
>gnl|CDD|178767 PLN03228, PLN03228, methylthioalkylmalate synthase; Provisional.
Length = 503
Score = 37.2 bits (86), Expect = 0.047
Identities = 29/113 (25%), Positives = 51/113 (45%), Gaps = 9/113 (7%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHP---DIPIHIHTHDTSGAGVASMIACAEAGADVVDVAV 526
D G+ P L+ ++ P DI +H H+ G A+ IA AGA V+V +
Sbjct: 260 DTVGINMPHEFGELVTYVKANTPGIDDIVFSVHCHNDLGLATANTIAGICAGARQVEVTI 319
Query: 527 DSMSGMTSQPSMGAVVASLQG------SDIDTGLDLKDISAYSAYWEQTRQLY 573
+ + + S+ VV +L+ + + TG+D + I A S ++ +Y
Sbjct: 320 NGIGERSGNASLEEVVMALKCRGAYLMNGVYTGIDTRQIMATSKMVQEYTGMY 372
>gnl|CDD|163685 cd07948, DRE_TIM_HCS, Saccharomyces cerevisiae homocitrate synthase
and related proteins, catalytic TIM barrel domain.
Homocitrate synthase (HCS) catalyzes the condensation of
acetyl-CoA and alpha-ketoglutarate to form homocitrate,
the first step in the lysine biosynthesis pathway. This
family includes the Yarrowia lipolytica LYS1 protein as
well as the Saccharomyces cerevisiae LYS20 and LYS21
proteins. This family belongs to the DRE-TIM
metallolyase superfamily. DRE-TIM metallolyases include
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 262
Score = 36.5 bits (85), Expect = 0.050
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAV 526
D G+ PR L+ +R I H H+ +G +A+ A EAGA +D V
Sbjct: 162 DTVGIATPRQVYELVRTLR-GVVSCDIEFHGHNDTGCAIANAYAALEAGATHIDTTV 217
>gnl|CDD|225141 COG2232, COG2232, Predicted ATP-dependent carboligase related to
biotin carboxylase [General function prediction only].
Length = 389
Score = 36.7 bits (85), Expect = 0.055
Identities = 44/209 (21%), Positives = 85/209 (40%), Gaps = 33/209 (15%)
Query: 100 GPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNG 159
G +E+ +E + +I K G GG +V ++ EE+
Sbjct: 133 GMPEPSEKKIEPLEEGEKTLILKPVSGAGG----LVELVKFDEEDPP------------P 176
Query: 160 AMFIEKFIERPRHIEVQLLGDKAGNVVHLYERDCSVQRRHQKVV-----EIAPAPHLDIN 214
++FIE R + V + + + + R + + P P+ ++
Sbjct: 177 GFIFQEFIE-GRPVSVSFISNGSDALTLAVNDQIIDGLRGEYSQFVYKGNLTPFPYEEVE 235
Query: 215 VRNKMTDLAVKLAKHVGYSNAGTVEFLCDESGQFYFIEVNARLQVEHTVTEEITGVDLVQ 274
+ LA +L + +G + V+F+ ++ G Y IEVN R+Q E +G++L +
Sbjct: 236 ---EAERLAEELVEELGLVGSNGVDFVLNDKG-PYVIEVNPRIQGTLECIERSSGINLFR 291
Query: 275 SQIRVAEGMTLPELGLTQEKISPQGFAIQ 303
I+ +G LP E+ P+G+A +
Sbjct: 292 LHIQAFDG-ELP------ERPKPRGYACK 313
>gnl|CDD|237001 PRK11856, PRK11856, branched-chain alpha-keto acid dehydrogenase
subunit E2; Reviewed.
Length = 411
Score = 36.3 bits (85), Expect = 0.085
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 923 GSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSI 965
G ++E VKVGD V++G L + K + + +PV G V +
Sbjct: 17 GEIVEWLVKVGDTVKEGQPLAEVETDKATVEIPSPVAGTVAKL 59
>gnl|CDD|215237 PLN02433, PLN02433, uroporphyrinogen decarboxylase.
Length = 345
Score = 36.1 bits (84), Expect = 0.093
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 15/74 (20%)
Query: 465 LINTFD-MAGLLKPR--------AAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACA 515
++ FD AG L P + ++ ++ +HPD+P+ ++ + SG + + A
Sbjct: 195 VVQIFDSWAGHLSPVDFEEFSKPYLEKIVDEVKARHPDVPLILYANG-SGGLLERL---A 250
Query: 516 EAGADVV--DVAVD 527
G DV+ D VD
Sbjct: 251 GTGVDVIGLDWTVD 264
>gnl|CDD|226135 COG3608, COG3608, Predicted deacylase [General function prediction
only].
Length = 331
Score = 35.8 bits (83), Expect = 0.10
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 907 PKAAKSVPG---QVGAPMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEMV---VQAPVQG 960
P ++P + AP G V E V +GDKVE G L + + ++APV G
Sbjct: 246 PTKGLALPSSDEMIRAPAGGLV-EFLVDLGDKVEAGDVLATIHDPPLGEGEAEIRAPVSG 304
Query: 961 VVKSIDASMLLRG 973
++ + + L++
Sbjct: 305 IIIARRSLRLVQP 317
>gnl|CDD|117020 pfam08443, RimK, RimK-like ATP-grasp domain. This ATP-grasp domain
is found in the ribosomal S6 modification enzyme RimK.
Length = 190
Score = 34.7 bits (80), Expect = 0.13
Identities = 43/207 (20%), Positives = 80/207 (38%), Gaps = 26/207 (12%)
Query: 78 GDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKY-GLPVIFKAAYGGGGRGMRVVR 136
DK + Q G+P VP T G + E+A +F + G PV+ K+ +G G G+ +
Sbjct: 2 RDKAKSHQLLAKHGIP-VPNT-GLAWSPEDAEKFIEQIKGFPVVVKSVFGSQGIGVFLA- 58
Query: 137 KMEDVEENFQRASSEAKAAFG-NGAMFIEKFIERP--RHIEVQLLGDKAGNVVHLYERDC 193
E+ Q +A + +++FI R I ++G + +H +
Sbjct: 59 ------EDEQSLEQLLEAFKWLKNQILVQEFIAEAGNRDIRCLVVGGEVVGAIHRQSNEG 112
Query: 194 SVQRRHQK--VVEIAPAPHLDINVRNKMTDLAVKLAKHVGYSNAGTVEFLCDESGQFYFI 251
+ + V E + + ++A+K A+ +G G F
Sbjct: 113 DFRTNLHRGGVAEP-------YQLSQEEEEIAIKAAQAMGLDVLGVDIFRSKRG--LLVC 163
Query: 252 EVNARLQVEHTVTEEITGVDLVQSQIR 278
EVN+ ++ E TG+++ I
Sbjct: 164 EVNSSPGLKG--IERTTGINIAIKLIE 188
>gnl|CDD|235577 PRK05718, PRK05718,
keto-hydroxyglutarate-aldolase/keto-deoxy-
phosphogluconate aldolase; Provisional.
Length = 212
Score = 34.4 bits (80), Expect = 0.18
Identities = 32/108 (29%), Positives = 51/108 (47%), Gaps = 19/108 (17%)
Query: 13 LVGKGLPPVEAYLNIP---EIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDAGIRFI-- 67
LV GLP +E L P E IR+ + +A+ G G + AQA+ +AG +FI
Sbjct: 36 LVAGGLPVLEVTLRTPAALEAIRLIAKEVPEAL-IGAGTVLNPEQLAQAI-EAGAQFIVS 93
Query: 68 -GPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLK 114
G +P +++ AA + +P++PG P + ME L+
Sbjct: 94 PGLTPPLLK----------AAQEGPIPLIPGVSTP-SELMLGMELGLR 130
>gnl|CDD|215533 PLN02983, PLN02983, biotin carboxyl carrier protein of acetyl-CoA
carboxylase.
Length = 274
Score = 34.8 bits (80), Expect = 0.21
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 907 PKAAKSVPGQVGAPMPGSVMEIR-------VKVGDKVEKGAALVVLSAMKMEMVVQAPVQ 959
KA KS + +PM G+ VKVGDKV+KG + ++ AMK+ ++A
Sbjct: 190 AKAPKSSHPPLKSPMAGTFYRSPAPGEPPFVKVGDKVQKGQVVCIIEAMKLMNEIEADQS 249
Query: 960 GVVKSIDA 967
G + I A
Sbjct: 250 GTIVEILA 257
>gnl|CDD|173033 PRK14569, PRK14569, D-alanyl-alanine synthetase A; Provisional.
Length = 296
Score = 34.7 bits (79), Expect = 0.25
Identities = 32/147 (21%), Positives = 63/147 (42%), Gaps = 22/147 (14%)
Query: 117 LPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEVQ 176
PV K + GG V+ +++++ ++ AS G + IE+++ + I V
Sbjct: 131 FPVAVKPSSGGSSIATFKVKSIQELKHAYEEASK-------YGEVMIEQWVT-GKEITVA 182
Query: 177 LLGDKAGNVVHL--------YERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLAVKLAK 228
++ D+ + V + YE S + + + L++ LA K
Sbjct: 183 IVNDEVYSSVWIEPQNEFYDYESKYSGKSIYHSPSGLCEQKELEVR------QLAKKAYD 236
Query: 229 HVGYSNAGTVEFLCDESGQFYFIEVNA 255
+G S V+F+ D+ G FY +E+N+
Sbjct: 237 LLGCSGHARVDFIYDDRGNFYIMEINS 263
>gnl|CDD|232916 TIGR00318, cyaB, adenylyl cyclase CyaB, putative. The protein CyaB
from Aeromonas hydrophila is a second adenylyl cyclase
from that species, as demonstrated by complementation in
E. coli and by assay of the enzymatic properties of
purified recombinant protein. It has no detectable
homology to any other protein of known function, and has
several unusual properties, including an optimal
temperature of 65 degrees and an optimal pH of 9.5. A
cluster of uncharaterized archaeal homologs may be
orthologous and serve (under certain circumstances) to
produce the regulatory metabolite cyclic AMP (cAMP)
[Regulatory functions, Small molecule interactions].
Length = 174
Score = 33.2 bits (76), Expect = 0.37
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 759 KLDTRIFLT--GPKVG------EEFEVKIQPPQGFRQILKSKGPEAFAKAVR 802
KL F+T GPK+ +E E KI+ + QILK G + + ++
Sbjct: 56 KLTGEKFVTYKGPKIDNESKTRKEIEFKIEDIENALQILKKLGFKKVYEVIK 107
>gnl|CDD|227003 COG4656, RnfC, Predicted NADH:ubiquinone oxidoreductase, subunit
RnfC [Energy production and conversion].
Length = 529
Score = 33.5 bits (77), Expect = 0.67
Identities = 25/86 (29%), Positives = 36/86 (41%), Gaps = 18/86 (20%)
Query: 905 IHPKAAKS----VPGQVGAPMP-----------GSVMEIRVKVGDKVEKGAALVVLSAMK 949
IHP K +P + AP+P G+ + VKVGDKV KG L
Sbjct: 10 IHPPENKHQSNILPIR-IAPLPQRALIPLKQHIGAPGILLVKVGDKVLKGQPLTR--GEG 66
Query: 950 MEMVVQAPVQGVVKSIDASMLLRGAN 975
+ + V AP G V +I+ + +
Sbjct: 67 IMLPVHAPTSGTVTAIEPANFPHPSG 92
>gnl|CDD|223871 COG0800, Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase
[Carbohydrate transport and metabolism].
Length = 211
Score = 32.6 bits (75), Expect = 0.72
Identities = 37/127 (29%), Positives = 49/127 (38%), Gaps = 31/127 (24%)
Query: 13 LVGKGLPPVEAYLNIP---EIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDAGIRFI-- 67
L+ G+P +E L P E IR + G G + QA+ AG +FI
Sbjct: 34 LIEGGIPAIEITLRTPAALEAIRALAKE-FPEALIGAGTVLNPEQARQAI-AAGAQFIVS 91
Query: 68 -GPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTE--EAMEF---CLKYGLPVIF 121
G +P V + AA G+P +PG T TE A+E LK F
Sbjct: 92 PGLNPEVAK----------AANRYGIPYIPGV---ATPTEIMAALELGASALK-----FF 133
Query: 122 KAAYGGG 128
A GG
Sbjct: 134 PAEVVGG 140
>gnl|CDD|233365 TIGR01347, sucB, 2-oxoglutarate dehydrogenase complex
dihydrolipoamide succinyltransferase (E2 component).
This model describes the TCA cycle 2-oxoglutarate system
E2 component, dihydrolipoamide succinyltransferase. It
is closely related to the pyruvate dehydrogenase E2
component, dihydrolipoamide acetyltransferase. The seed
for this model includes mitochondrial and Gram-negative
bacterial forms. Mycobacterial candidates are highly
derived, differ in having and extra copy of the
lipoyl-binding domain at the N-terminus. They score
below the trusted cutoff, but above the noise cutoff and
above all examples of dihydrolipoamide acetyltransferase
[Energy metabolism, TCA cycle].
Length = 403
Score = 33.2 bits (76), Expect = 0.77
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 920 PMPGSVMEIRV-----KVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSIDAS 968
+ S+ E V KVGD V++ +V + K+ + V +P GV++ I
Sbjct: 7 ELAESITEGTVAEWHKKVGDTVKRDENIVEIETDKVVLEVPSPADGVLQEILFK 60
>gnl|CDD|218801 pfam05896, NQRA, Na(+)-translocating NADH-quinone reductase subunit
A (NQRA). This family consists of several bacterial
Na(+)-translocating NADH-quinone reductase subunit A
(NQRA) proteins. The Na(+)-translocating NADH:
ubiquinone oxidoreductase (Na(+)-NQR) generates an
electrochemical Na(+) potential driven by aerobic
respiration.
Length = 257
Score = 32.9 bits (76), Expect = 0.78
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 930 VKVGDKVEKGAALVVLSAMKME-MVVQAPVQGVVKSIDASMLLRGA 974
VK GDKV+ G L K + AP G V +I+ RGA
Sbjct: 45 VKEGDKVKAGQPL--FEDKKNPGVKFTAPASGTVVAIN-----RGA 83
>gnl|CDD|237068 PRK12344, PRK12344, putative alpha-isopropylmalate/homocitrate
synthase family transferase; Provisional.
Length = 524
Score = 33.1 bits (77), Expect = 0.80
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 490 KHPDIPIHIHTHDTSGAGVASMIACAEAGA 519
P +P+ IH H+ SG VA+ +A EAGA
Sbjct: 198 AAPGVPLGIHAHNDSGCAVANSLAAVEAGA 227
>gnl|CDD|219688 pfam07994, NAD_binding_5, Myo-inositol-1-phosphate synthase. This
is a family of myo-inositol-1-phosphate synthases.
Inositol-1-phosphate catalyzes the conversion of
glucose-6- phosphate to inositol-1-phosphate, which is
then dephosphorylated to inositol. Inositol phosphates
play an important role in signal transduction.
Length = 389
Score = 33.0 bits (76), Expect = 0.80
Identities = 21/76 (27%), Positives = 29/76 (38%), Gaps = 3/76 (3%)
Query: 20 PVEAYLNIPEIIRVAKENDVDAIHPGYGFLSERSDFAQAVLDAGIRFIGPSPYVVQQMGD 79
P E Y + + EN + AI + S + +A A L AG FI SP
Sbjct: 143 PTERYAPVIPGVNDTAENLLKAIKNNHEEESASTLYAYAALLAGCAFINGSP--QNTASV 200
Query: 80 KVAARQAAIDSGVPIV 95
A + G+PI
Sbjct: 201 PGLIEL-AEEKGLPIA 215
Score = 29.9 bits (68), Expect = 7.9
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 85 QAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVI 120
AA+ +G + G+P + +E + GLP+
Sbjct: 180 YAALLAGCAFINGSPQNTASVPGLIELAEEKGLPIA 215
>gnl|CDD|234864 PRK00915, PRK00915, 2-isopropylmalate synthase; Validated.
Length = 513
Score = 33.2 bits (77), Expect = 0.82
Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 466 INTFDMAGLLKPRAAKLLIGAIREKHPDI---PIHIHTHDTSGAGVASMIACAEAGADVV 522
IN D G P LI +RE+ P+I I +H H+ G VA+ +A EAGA V
Sbjct: 166 INIPDTVGYTTPEEFGELIKTLRERVPNIDKAIISVHCHNDLGLAVANSLAAVEAGARQV 225
Query: 523 DVAV 526
+ +
Sbjct: 226 ECTI 229
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 33.2 bits (77), Expect = 0.85
Identities = 17/75 (22%), Positives = 26/75 (34%), Gaps = 12/75 (16%)
Query: 87 AIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQ 146
+D V +V G TE KYG+P I V KM+ +F
Sbjct: 83 VLDGAVVVVCAVGGVEPQTETVWRQAEKYGVPRII------------FVNKMDRAGADFF 130
Query: 147 RASSEAKAAFGNGAM 161
R ++ + G +
Sbjct: 131 RVLAQLQEKLGAPVV 145
>gnl|CDD|218143 pfam04551, GcpE, GcpE protein. In a variety of organisms,
including plants and several eubacteria, isoprenoids are
synthesised by the mevalonate-independent
2-C-methyl-D-erythritol 4-phosphate (MEP) pathway.
Although different enzymes of this pathway have been
described, the terminal biosynthetic steps of the MEP
pathway have not been fully elucidated. GcpE gene of
Escherichia coli is involved in this pathway.
Length = 345
Score = 32.9 bits (76), Expect = 0.86
Identities = 14/31 (45%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 499 HTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
T D A VA + EAG D+V VAV M
Sbjct: 26 DTRDVE-ATVAQIKRLEEAGCDIVRVAVPDM 55
>gnl|CDD|129128 TIGR00017, cmk, cytidylate kinase. This family consists of
cytidylate kinase, which catalyzes the phosphorylation
of cytidine 5-monophosphate (dCMP) to cytidine 5
-diphosphate (dCDP) in the presence of ATP or GTP. UMP
and dCMP can also act as acceptors [Purines,
pyrimidines, nucleosides, and nucleotides, Nucleotide
and nucleoside interconversions].
Length = 217
Score = 32.4 bits (74), Expect = 0.88
Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 4/81 (4%)
Query: 164 EKFIERPRHIEVQLLGDKAGNVVHLYERDCSVQRRHQKVVEIAPAPHLDINVRNKMTDLA 223
+ E H++++ + V L D S R Q+V A + VR +
Sbjct: 55 DALAELISHLDIRFIPTNGEVEVFLNGEDVSEAIRTQEVANAASKVAVFPKVREALLKRQ 114
Query: 224 VKLAKHVGY----SNAGTVEF 240
LAK+ G + GTV F
Sbjct: 115 QALAKNDGIIADGRDIGTVVF 135
>gnl|CDD|198252 cd10389, SH2_SHB, Src homology 2 domain found in SH2
domain-containing adapter protein B (SHB). SHB
functions in generating signaling compounds in response
to tyrosine kinase activation. SHB contains
proline-rich motifs, a phosphotyrosine binding (PTB)
domain, tyrosine phosphorylation sites, and a SH2
domain. SHB mediates certain aspects of
platelet-derived growth factor (PDGF) receptor-,
fibroblast growth factor (FGF) receptor-, neural growth
factor (NGF) receptor TRKA-, T cell receptor-,
interleukin-2 (IL-2) receptor- and focal adhesion
kinase- (FAK) signaling. SRC-like FYN-Related Kinase
FRK/RAK (also named BSK/IYK or GTK) and SHB regulate
apoptosis, proliferation and differentiation. SHB
promotes apoptosis and is also required for proper
mitogenicity, spreading and tubular morphogenesis in
endothelial cells. SHB also plays a role in preventing
early cavitation of embryoid bodies and reduces
differentiation to cells expressing albumin, amylase,
insulin and glucagon. SHB is a multifunctional protein
that has difference responses in different cells under
various conditions. In general SH2 domains are involved
in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 97
Score = 30.8 bits (69), Expect = 1.0
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 1 MHMHRQKADESYLVGKGLPPVEAYLNIPEII 31
MHM K E Y++G+ PP ++ +PE+I
Sbjct: 48 MHMKLAKTKEKYVLGQNSPPFDS---VPEVI 75
>gnl|CDD|235426 PRK05352, PRK05352, Na(+)-translocating NADH-quinone reductase
subunit A; Provisional.
Length = 448
Score = 32.5 bits (75), Expect = 1.2
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 6/45 (13%)
Query: 930 VKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSIDASMLLRGA 974
VK GDKV+KG L + +P G V +I+ RG
Sbjct: 46 VKEGDKVKKGQPLFE-DKKNPGVKFTSPASGTVVAIN-----RGE 84
>gnl|CDD|183087 PRK11325, PRK11325, scaffold protein; Provisional.
Length = 127
Score = 30.7 bits (70), Expect = 1.4
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 907 PKAAKSV-PGQVGAPMPGSVMEIRVKVGDK 935
K +V G VGAP G VM++++KV D+
Sbjct: 21 DKNDPNVGTGMVGAPACGDVMKLQIKVNDE 50
>gnl|CDD|234644 PRK00115, hemE, uroporphyrinogen decarboxylase; Validated.
Length = 346
Score = 32.0 bits (74), Expect = 1.6
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 19/70 (27%)
Query: 469 FDM-AGLLKPRA--------AKLLIGAIREKHPDIPIHIHTHDTSGAG--VASMIACAEA 517
FD AG L P K ++ ++ +HPD+P+ GAG + +M AE
Sbjct: 206 FDSWAGALSPADYREFVLPYMKRIVAELKREHPDVPV---ILFGKGAGELLEAM---AET 259
Query: 518 GADVVDVAVD 527
GADV V +D
Sbjct: 260 GADV--VGLD 267
>gnl|CDD|176112 cd08420, PBP2_CysL_like, C-terminal substrate binding domain of
LysR-type transcriptional regulator CysL, which
activates the transcription of the cysJI operon encoding
sulfite reductase, contains the type 2 periplasmic
binding fold. CysL, also known as YwfK, is a regular of
sulfur metabolism in Bacillus subtilis. Sulfur is
required for the synthesis of proteins and essential
cofactors in all living organism. Sulfur can be
assimilated either from inorganic sources (sulfate and
thiosulfate), or from organic sources (sulfate esters,
sulfamates, and sulfonates). CysL activates the
transcription of the cysJI operon encoding sulfite
reductase, which reduces sulfite to sulfide. Both cysL
mutant and cysJI mutant are unable to grow using sulfate
or sulfite as the sulfur source. Like other LysR-type
regulators, CysL also negatively regulates its own
transcription. In Escherichia coli, three LysR-type
activators are involved in the regulation of sulfur
metabolism: CysB, Cbl and MetR. The topology of this
substrate-binding domain is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis.
Length = 201
Score = 31.3 bits (72), Expect = 1.6
Identities = 6/44 (13%), Positives = 20/44 (45%), Gaps = 7/44 (15%)
Query: 483 LIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAV 526
L+ R+++P++ + + +T +A + +D+ +
Sbjct: 18 LLARFRKRYPEVRVSLTIGNT--EEIAERVL-----DGEIDLGL 54
>gnl|CDD|199871 cd06251, M14_ASTE_ASPA_like_1, Peptidase M14 Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA)-like;
uncharacterized subgroup. A functionally
uncharacterized subgroup of the Succinylglutamate
desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily
which is part of the M14 family of
metallocarboxypeptidases. ASTE catalyzes the fifth and
last step in arginine catabolism by the arginine
succinyltransferase pathway, and aspartoacylase (ASPA,
also known as aminoacylase 2, and ACY-2; EC:3.5.1.15)
cleaves N-acetyl L-aspartic acid (NAA) into aspartate
and acetate. NAA is abundant in the brain, and
hydrolysis of NAA by ASPA may help maintain white
matter. ASPA is an NAA scavenger in other tissues.
Mutations in the gene encoding ASPA cause Canavan
disease (CD), a fatal progressive neurodegenerative
disorder involving dysmyelination and spongiform
degeneration of white matter in children. This enzyme
binds zinc which is necessary for activity. Measurement
of elevated NAA levels in urine is used in the diagnosis
of CD.
Length = 287
Score = 31.7 bits (73), Expect = 1.6
Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 917 VGAPMPGSVMEIRVKVGDKVEKGAALVVLS--AMKMEMVVQAPVQGVV 962
V AP G ++ VK+GD+VEKG L ++ + E V+AP G+V
Sbjct: 222 VRAPRGG-LLRSLVKLGDRVEKGQLLATITDPFGEEEAEVKAPFDGIV 268
>gnl|CDD|222084 pfam13375, RnfC_N, RnfC Barrel sandwich hybrid domain. This domain
is part of the barrel sandwich hybrid superfamily. It is
found at the N-terminus of the RnfC Electron transport
complex protein. It appears to be most related to the
N-terminal NQRA domain (pfam05896).
Length = 101
Score = 30.1 bits (69), Expect = 1.6
Identities = 24/80 (30%), Positives = 35/80 (43%), Gaps = 23/80 (28%)
Query: 905 IHPKAAKS-----------VPGQVGAPMP---GSVMEIRVKVGDKVEKGAALV----VLS 946
IHP K +P ++ P+ G+ + VKVGD+V KG + +S
Sbjct: 7 IHPPENKELSNDKPIEKLPLPKELVIPLSQHIGAPAKPLVKVGDRVLKGQKIAEADGFVS 66
Query: 947 AMKMEMVVQAPVQGVVKSID 966
A V A V G VK+I+
Sbjct: 67 AP-----VHASVSGTVKAIE 81
>gnl|CDD|176554 cd08613, GDPD_GDE4_like_1, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial homologs of
mammalian glycerophosphodiester phosphodiesterase GDE4.
This subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized bacterial homologs of mammalian GDE4, a
transmembrane protein whose cellular function has not
been elucidated yet.
Length = 309
Score = 31.9 bits (73), Expect = 1.6
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 5/54 (9%)
Query: 758 DKLDTRIFLTGPKVGEEFEVKIQPPQGFRQILKSKGPEAFAKAVRQNKSLLLMD 811
+ TR+ L GP G EF P+ +++ PE F + NK L
Sbjct: 261 EAAGTRVILVGPYTGGEFSEGFDTPEDLKRL-----PEGFTGYIWTNKIEALAP 309
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 32.6 bits (74), Expect = 1.6
Identities = 23/92 (25%), Positives = 39/92 (42%), Gaps = 22/92 (23%)
Query: 766 LTG--PKVGEEFEVKIQPPQGFRQILKSKGPEAFAKAVR--------------------Q 803
+TG P+V E FE + P+ + + G +F K +R +
Sbjct: 2643 ITGGLPRVSELFEARKPKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRSMDYFVDK 2702
Query: 804 NKSLLLMDTTFRDAHQSLLATRVRSHDLLKIS 835
K +L+ F A +++ V SHD+L+IS
Sbjct: 2703 GKQILVHADEFVHAGEAMTDGVVSSHDILRIS 2734
>gnl|CDD|188192 TIGR01999, iscU, FeS cluster assembly scaffold IscU. This model
represents IscU, a homolog of the N-terminal region of
NifU, an Fe-S cluster assembly protein found mostly in
nitrogen-fixing bacteria. IscU is considered part of the
IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU
is found in nitrogenase-containing (nitrogen-fixing)
species. A NifU-type protein is also found in
Helicobacter and Campylobacter. IscU and NifU are
considered scaffold proteins on which Fe-S clusters are
assembled before transfer to apoproteins. This model
excludes true NifU proteins as in Klebsiella pneumoniae
and Anabaena sp. as well as archaeal homologs. It
includes largely proteobacterial and eukaryotic forms
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 124
Score = 30.5 bits (69), Expect = 2.0
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 907 PKAAKSV-PGQVGAPMPGSVMEIRVKVGDK 935
K K+V G VGAP G VM++++KV D
Sbjct: 19 DKDDKNVGTGLVGAPACGDVMKLQIKVNDD 48
>gnl|CDD|130050 TIGR00977, LeuA_rel, 2-isopropylmalate synthase/homocitrate
synthase family protein. This model represents
uncharacterized proteins related to 2-isopropylmalate
synthases and homocitrate synthases but phylogenetically
distint. Each species represented in the seed alignment
also has a member of a known family of 2-isopropylmalate
synthases [Unknown function, General].
Length = 526
Score = 31.8 bits (72), Expect = 2.6
Identities = 17/77 (22%), Positives = 33/77 (42%)
Query: 470 DMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAVDSM 529
D G P + ++ + IH H+ SG VA+ + EAGA +V ++
Sbjct: 175 DTNGGTLPHEISEITTKVKRSLKQPQLGIHAHNDSGTAVANSLLAVEAGATMVQGTINGY 234
Query: 530 SGMTSQPSMGAVVASLQ 546
++ +++ +LQ
Sbjct: 235 GERCGNANLCSLIPNLQ 251
>gnl|CDD|225018 COG2107, COG2107, Predicted periplasmic solute-binding protein
[General function prediction only].
Length = 272
Score = 31.1 bits (71), Expect = 3.0
Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 25/68 (36%)
Query: 712 PFDFGKLKTELQERH----------------PEATDRDVMSAALYPQVTEDYL------T 749
GK+KT L + + T +SAA YP + +DY +
Sbjct: 19 AIVEGKIKTPLLYQEVIADIETLNREALEGRYDVT---AISAAAYPYIADDYALLRSGAS 75
Query: 750 FRESFGPV 757
+GP+
Sbjct: 76 LGIGYGPI 83
>gnl|CDD|176145 cd08456, PBP2_LysR, The C-terminal substrate binding domain of
LysR, transcriptional regulator for lysine biosynthesis,
contains the type 2 periplasmic binding fold. LysR, the
transcriptional activator of lysA encoding
diaminopimelate decarboxylase, catalyses the
decarboxylation of diaminopimelate to produce lysine.
The LysR-transcriptional regulators comprise the largest
family of prokaryotic transcription factor. Homologs of
some of LTTRs with similar domain organizations are also
found in the archaea and eukaryotic organisms. The LTTRs
are composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The genes controlled by the
LTTRs have diverse functional roles including amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to a name a few. This substrate-binding domain
shows significant homology to the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 196
Score = 30.5 bits (69), Expect = 3.2
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 471 MAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTS 504
++ PRA I A ++HPD+ I IHT D+
Sbjct: 10 LSQSFLPRA----IKAFLQRHPDVTISIHTRDSP 39
>gnl|CDD|235289 PRK04350, PRK04350, thymidine phosphorylase; Provisional.
Length = 490
Score = 31.3 bits (72), Expect = 3.4
Identities = 14/26 (53%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 918 GAPM-PGSVMEIRVKVGDKVEKGAAL 942
GAP G+ +++ VKVGDKV+KG L
Sbjct: 432 GAPKDKGAGIDLHVKVGDKVKKGDPL 457
>gnl|CDD|234495 TIGR04192, GRASP_w_spasm, ATP-GRASP peptide maturase,
grasp-with-spasm system. Members of this protein family
are ATP-GRASP proteins that occur in a peptide
maturation cassette with a SPASM domain protein. SPASM
(TIGR04085) usually occurs as a C-terminal extension to
radical SAM enzymes that act as peptide maturases,
although it can occur independently.
Length = 318
Score = 30.9 bits (70), Expect = 3.5
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 234 NAGTVEFLCDESGQFYFIEVNA 255
N G+++F+ E +FYF+EVN
Sbjct: 274 NCGSLDFIVTEDNEFYFLEVNP 295
>gnl|CDD|218779 pfam05853, DUF849, Prokaryotic protein of unknown function
(DUF849). This family consists of several hypothetical
prokaryotic proteins with no known function.
Length = 273
Score = 30.9 bits (71), Expect = 3.7
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 8/40 (20%)
Query: 485 GAI--REKHPDIPIHIHTHDTSGAGVASMIACAEAGADVV 522
GAI P +P+ T +A AEAGA +V
Sbjct: 10 GAIHTPSDSPALPV------TPEEIAEEAVAAAEAGAAIV 43
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 30.3 bits (69), Expect = 3.8
Identities = 17/73 (23%), Positives = 24/73 (32%), Gaps = 17/73 (23%)
Query: 86 AAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKM-----ED 140
A D + +V G T E + L GLP+I V K+ ED
Sbjct: 84 AQADGALLVVDANEGVEPQTREHLNIALAGGLPIIV------------AVNKIDRVGEED 131
Query: 141 VEENFQRASSEAK 153
+E + K
Sbjct: 132 FDEVLREIKELLK 144
>gnl|CDD|237370 PRK13380, PRK13380, glycine cleavage system protein H; Provisional.
Length = 144
Score = 30.0 bits (68), Expect = 3.9
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 917 VGAPMPGSVMEIRVK-VGDKVEKGAALVVLSAMKMEMVVQAPVQGVV 962
M G V+ +R+K +G KVEKG + L + K V AP+ G V
Sbjct: 38 YAQTMAGDVVFVRLKELGKKVEKGKPVATLESGKWAGPVPAPLTGEV 84
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 30.7 bits (70), Expect = 4.6
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 923 GSVMEIRVKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSID 966
G+ E+ VKVGD+V KG L +M + V AP G V +I+
Sbjct: 46 GAEGELCVKVGDRVLKGQPL-TQGDGRMSLPVHAPTSGTVVAIE 88
>gnl|CDD|235605 PRK05782, PRK05782, bifunctional sirohydrochlorin cobalt
chelatase/precorrin-8X methylmutase; Validated.
Length = 335
Score = 30.5 bits (69), Expect = 5.0
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 62 AGIRF-IGPSPYVVQQMGDKVAARQAAID-----SGVPIVPGTPGPITTTEEAMEFCLKY 115
A +R +G VV +G+ A + +P + TP T +E E ++
Sbjct: 247 AAMRLSLGQGGKVVV-IGNAPTALIETLKLVKEGVDIPFIVATPPGFTNAKEVKEALIES 305
Query: 116 GLP-VIFKAAYGGGG 129
G+P V+ + YGG G
Sbjct: 306 GIPSVVLRGTYGGSG 320
>gnl|CDD|220833 pfam10646, Germane, Sporulation and spore germination. The GerMN
domain is a region of approximately 100 residues that is
found, duplicated, in the Bacillus GerM protein and is
implicated in both sporulation and spore germination.
The domain is found in a number of different bacterial
species both alone and in association with other domains
such as Amidase_3 pfam01520, Gmad1 and Gmad2. It is
predicted to have a novel alpha-beta fold.
Length = 116
Score = 28.8 bits (65), Expect = 5.4
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 12/56 (21%)
Query: 407 YFIDEN-----PQLFTLQPTKNRAQKLLNYLGTVLVNGPSTPLA---TPLLPAEVT 454
YF+D + P + T + A L L + GPS LA +LP
Sbjct: 4 YFVDPDGTKLVPVTRWVPKTDSLATAALEEL----LKGPSDELAPGLVSVLPPGTK 55
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 29.8 bits (68), Expect = 5.6
Identities = 15/82 (18%), Positives = 26/82 (31%), Gaps = 15/82 (18%)
Query: 82 AARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDV 141
A QA D + +V G + T E + G+P+I + K++ V
Sbjct: 86 GASQA--DGAILVVDAVEGVMPQTREHLLLAKTLGVPIIV------------FINKIDRV 131
Query: 142 -EENFQRASSEAKAAFGNGAMF 162
+ + E F
Sbjct: 132 DDAELEEVVEEISRELLEKYGF 153
>gnl|CDD|176131 cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator, contains the type 2 periplasmic binding fold.
LysR-transcriptional regulators comprise the largest
family of prokaryotic transcription factor. Homologs of
some of LTTRs with similar domain organizations are also
found in the archaea and eukaryotic organisms. The LTTRs
are composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The genes controlled by the
LTTRs have diverse functional roles including amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to a name a few. This substrate-binding domain
shows significant homology to the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 197
Score = 29.8 bits (68), Expect = 5.7
Identities = 17/77 (22%), Positives = 27/77 (35%), Gaps = 18/77 (23%)
Query: 479 AAKLL---IGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVAV----DSMSG 531
AA LL + A R +HP I + + D S V + E VD + ++
Sbjct: 11 AATLLPPVLAAFRRRHPGIRVRL--RDVSAEQVIEAVRSGE-----VDFGIGSEPEADPD 63
Query: 532 MTSQP----SMGAVVAS 544
+ +P V
Sbjct: 64 LEFEPLLRDPFVLVCPK 80
>gnl|CDD|233649 TIGR01945, rnfC, electron transport complex, RnfABCDGE type, C
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of SoxR),
reduces the 2Fe-2S-containing superoxide sensor SoxR,
active as a transcription factor when oxidized. This
family of putative NADH oxidoreductase complexes exists
in many of the same species as the related NQR, a
Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the C subunit [Energy
metabolism, Electron transport].
Length = 435
Score = 30.4 bits (69), Expect = 5.8
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 930 VKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSIDA 967
VKVGDKV KG + + AP G V +I+
Sbjct: 47 VKVGDKVLKGQKIAKADGFVS-APIHAPTSGTVVAIEE 83
>gnl|CDD|188170 TIGR01832, kduD, 2-deoxy-D-gluconate 3-dehydrogenase. This model
describes 2-deoxy-D-gluconate 3-dehydrogenase (also
called 2-keto-3-deoxygluconate oxidoreductase), a member
of the family of short-chain-alcohol dehydrogenases
(pfam00106). This protein has been characterized in
Erwinia chrysanthemi as an enzyme of pectin degradation
[Energy metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 248
Score = 30.1 bits (68), Expect = 5.9
Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 6/74 (8%)
Query: 504 SGAGVASMIACAEAGADVVDVAVDSMSGMTSQPSMGAVVASLQGSDIDTGLDLKDISAYS 563
+G G + AEAGAD+V S Q V +L + DL DI A
Sbjct: 15 TGLGQGIAVGLAEAGADIVGAGRSEPSETQQQ------VEALGRRFLSLTADLSDIEAIK 68
Query: 564 AYWEQTRQLYAPFE 577
A + + + +
Sbjct: 69 ALVDSAVEEFGHID 82
>gnl|CDD|150551 pfam09891, DUF2118, Uncharacterized protein conserved in archaea
(DUF2118). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 149
Score = 29.3 bits (66), Expect = 6.0
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 920 PMPGSVMEIRVKVGDKVEKGAALVVLSAMKMEM-VVQAPVQGVVKSID 966
P G + V GD+V KG L ++ K E+ V++PV+G V I+
Sbjct: 85 PAEGYKVYPIVDEGDRVLKGDRLAAVTTRKGEVRYVRSPVEGTVVFIN 132
>gnl|CDD|163650 cd07407, MPP_YHR202W_N, Saccharomyces cerevisiae YHR202W and
related proteins, N-terminal metallophosphatase domain.
YHR202W is an uncharacterized Saccharomyces cerevisiae
UshA-like protein with two domains, an N-terminal
metallophosphatase domain and a C-terminal nucleotidase
domain. The N-terminal metallophosphatase domain
belongs to a large superfamily of distantly related
metallophosphatases (MPPs) that includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 282
Score = 30.0 bits (68), Expect = 6.1
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 3/24 (12%)
Query: 481 KLLIGAIREKHPDIPIHI---HTH 501
K+L AIR+ PD PI H+H
Sbjct: 206 KVLHDAIRKIFPDTPIQFLGGHSH 229
>gnl|CDD|223583 COG0509, GcvH, Glycine cleavage system H protein (lipoate-binding)
[Amino acid transport and metabolism].
Length = 131
Score = 29.2 bits (66), Expect = 6.2
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 931 KVGDKVEKGAALVVLSAMKMEMVVQAPVQGVV 962
+VG +V+ G +L V+ ++K V APV G V
Sbjct: 48 EVGAEVKAGESLAVVESVKAASDVYAPVSGEV 79
>gnl|CDD|184751 PRK14571, PRK14571, D-alanyl-alanine synthetase A; Provisional.
Length = 299
Score = 30.2 bits (68), Expect = 6.2
Identities = 51/208 (24%), Positives = 85/208 (40%), Gaps = 27/208 (12%)
Query: 57 QAVLDA-GIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPGTPGPITTTEEAMEFCLKY 115
QA+LD GIR+ G + DK+ + + V I P + E
Sbjct: 72 QAILDFLGIRYTGSDAFSSMICFDKLLTYRF-LKGTVEI----PDFVEIKEFMKT--SPL 124
Query: 116 GLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMFIEKFIERPRHIEV 175
G P + K G G+ + + +E FQ A E +G ++ ++++I R + V
Sbjct: 125 GYPCVVKPRREGSSIGVFIC----ESDEEFQHALKEDLPRYG--SVIVQEYIP-GREMTV 177
Query: 176 QLLGDKAGNVVHLYERDCSVQRRHQKVVE---------IAPAPHLDINVRNKMTDLAVKL 226
+L + G V L + +RR V I PAP L+ + + A+K
Sbjct: 178 SILETEKGFEV-LPILELRPKRRFYDYVAKYTKGETEFILPAP-LNPEEERLVKETALKA 235
Query: 227 AKHVGYSNAGTVEFLCDESGQFYFIEVN 254
G G V+ + + G+FYF+E+N
Sbjct: 236 FVEAGCRGFGRVDGIFSD-GRFYFLEIN 262
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 30.3 bits (69), Expect = 6.3
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 488 REKHPDIPIH----IHTHDTSGAGVASMIACAEAGADVVDVAVD 527
R + P+ + T +SG G A+ I AEAGA V VA +
Sbjct: 361 RRRDLRGPLVGKVVLITGASSGIGRATAIKVAEAGATVFLVARN 404
>gnl|CDD|180985 PRK07455, PRK07455,
keto-hydroxyglutarate-aldolase/keto-deoxy-
phosphogluconate aldolase; Provisional.
Length = 187
Score = 29.6 bits (67), Expect = 7.0
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 15/86 (17%)
Query: 45 GYGFLSERSDFAQAVLDAGIRFIGPSPYVVQQMGDKVAARQAAIDSGVPIVPG--TPGPI 102
G G + D +A+ AG +F +P+V ++ +AA+ +PI+PG TP I
Sbjct: 67 GTGTILTLEDLEEAI-AAGAQF-CFTPHVDPEL------IEAAVAQDIPIIPGALTPTEI 118
Query: 103 TTTEEAMEFCLKYGLPVIFKAAYGGG 128
T +A C+K +F GG
Sbjct: 119 VTAWQAGASCVK-----VFPVQAVGG 139
>gnl|CDD|221277 pfam11863, DUF3383, Protein of unknown function (DUF3383). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and viruses. Proteins
in this family are typically between 356 to 501 amino
acids in length.
Length = 478
Score = 30.1 bits (68), Expect = 7.3
Identities = 18/63 (28%), Positives = 23/63 (36%), Gaps = 4/63 (6%)
Query: 93 PIVPGTPGPITTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEA 152
IV G +A F G +IF + +R EDV +F S E
Sbjct: 4 RIVNVNIGVSAAAAQARGF----GALLIFTSNVIDPKERVREYSSAEDVGADFGTTSPEY 59
Query: 153 KAA 155
KAA
Sbjct: 60 KAA 62
>gnl|CDD|222161 pfam13477, Glyco_trans_4_2, Glycosyl transferase 4-like.
Length = 139
Score = 28.8 bits (65), Expect = 7.6
Identities = 21/85 (24%), Positives = 29/85 (34%), Gaps = 25/85 (29%)
Query: 466 INTFDMAGLLKPRAAKLLIGAIREKHPDIPIHIHTHDTSGAGVASMIACAEAGADVVDVA 525
I LK K LI I+ PDI +H H G+ +A
Sbjct: 52 IPRKGPFEYLKLFRLKKLIKKIK---PDI---VHAHYAKPYGLLGRLAA----------- 94
Query: 526 VDSMSGMTSQPSMGAVVASLQGSDI 550
+SG+ V+ S+ GSD
Sbjct: 95 --RLSGVIP------VILSVWGSDF 111
>gnl|CDD|240077 cd04726, KGPDC_HPS, 3-Keto-L-gulonate 6-phosphate decarboxylase
(KGPDC) and D-arabino-3-hexulose-6-phosphate synthase
(HPS). KGPDC catalyzes the formation of L-xylulose
5-phosphate and carbon dioxide from 3-keto-L-gulonate
6-phosphate as part of the anaerobic pathway for
L-ascorbate utilization in some eubacteria. HPS
catalyzes the formation of
D-arabino-3-hexulose-6-phosphate from D-ribulose
5-phosphate and formaldehyde in microorganisms that can
use formaldehyde as a carbon source. Both catalyze
reactions that involve the Mg2+-assisted formation and
stabilization of 1,2-enediolate reaction intermediates.
Length = 202
Score = 29.5 bits (67), Expect = 7.6
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 10/75 (13%)
Query: 484 IGAIREKHPDIPI--HIHTHDTSGAGVASMIACAEAGADVVDVAVDSMSGMTSQPSMGAV 541
+ A+RE PD I + T D GA A M +AGAD+V V G ++
Sbjct: 44 VRALREAFPDKIIVADLKTADA-GALEAEM--AFKAGADIVTV-----LGAAPLSTIKKA 95
Query: 542 VASLQGSDIDTGLDL 556
V + + + +DL
Sbjct: 96 VKAAKKYGKEVQVDL 110
>gnl|CDD|218675 pfam05648, PEX11, Peroxisomal biogenesis factor 11 (PEX11). This
family consists of several peroxisomal biogenesis factor
11 (PEX11) proteins from several eukaryotic species. The
PEX11 peroxisomal membrane proteins promote peroxisome
division in multiple eukaryotes.
Length = 225
Score = 29.5 bits (67), Expect = 8.6
Identities = 9/51 (17%), Positives = 17/51 (33%), Gaps = 4/51 (7%)
Query: 967 ASMLLRGANAVGYTNYPDNVVYKFCDLSVQVGM--DVFRVFDSLNYLPNLI 1015
AS LL ++ + +L Q + + R+ L +L
Sbjct: 24 ASRLLAWYLY--RKGSSPELIARLKNLESQFSLSRKLLRLGKFLEHLQAAA 72
>gnl|CDD|223347 COG0269, SgbH, 3-hexulose-6-phosphate synthase and related proteins
[Carbohydrate transport and metabolism].
Length = 217
Score = 29.1 bits (66), Expect = 8.8
Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 10/75 (13%)
Query: 484 IGAIREKHPDIPI--HIHTHDTSGAGVASMIACAEAGADVVDVAVDSMSGMTSQPSMGAV 541
+ A+RE PD I + T D GA A M EAGAD V V G ++
Sbjct: 47 VRALRELFPDKIIVADLKTADA-GAIEARM--AFEAGADWVTV-----LGAADDATIKKA 98
Query: 542 VASLQGSDIDTGLDL 556
+ + + +DL
Sbjct: 99 IKVAKEYGKEVQIDL 113
>gnl|CDD|189911 pfam01256, Carb_kinase, Carbohydrate kinase. This family is
related to pfam02110 and pfam00294 implying that it also
is a carbohydrate kinase. (personal obs Yeats C).
Length = 242
Score = 29.3 bits (66), Expect = 9.3
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 501 HDTSGAGVASMIACAEAGADVVDVAVDS 528
D +GA + + +A +GA +V VA DS
Sbjct: 8 KDYTGAPLLAALAALRSGAGLVSVATDS 35
>gnl|CDD|181324 PRK08251, PRK08251, short chain dehydrogenase; Provisional.
Length = 248
Score = 29.5 bits (67), Expect = 9.3
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 717 KLKTELQERHPEATDRDVMSAAL----YPQVTEDYLTFRESFGPVDKL 760
+LK EL R+P V AAL + QV E + FR+ G +D++
Sbjct: 41 ELKAELLARYPGIK---VAVAALDVNDHDQVFEVFAEFRDELGGLDRV 85
>gnl|CDD|184875 PRK14875, PRK14875, acetoin dehydrogenase E2 subunit
dihydrolipoyllysine-residue acetyltransferase;
Provisional.
Length = 371
Score = 29.5 bits (67), Expect = 9.4
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 930 VKVGDKVEKGAALVVLSAMKMEMVVQAPVQGVVKSIDAS 968
V+ GD+VEKG L+ + K+ V+AP G ++ A
Sbjct: 24 VQEGDEVEKGDELLDVETDKITNEVEAPAAGTLRRQVAQ 62
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 29.9 bits (67), Expect = 9.5
Identities = 35/142 (24%), Positives = 55/142 (38%), Gaps = 12/142 (8%)
Query: 633 IKVTPSSKVVGDFAQFMVQNKLTSEEVLARAEELSFPKSVVEFLQGAIGTPYQGFPEPLR 692
+KV +S G + T+EEV A L V E + I T + +PL
Sbjct: 1848 LKVIHTSVWAGQKRLIQLAKWKTAEEVFALGRSLP----VEEQPKQIIVTR-KSMLDPLE 1902
Query: 693 SKVLKDMPRIEGRPGASLPPFDFGKLKTELQERHPEATDRDVMSAALYPQVTEDYLTFRE 752
+L D P I R PF ++++ AT+ ++ LY +D+L
Sbjct: 1903 VHIL-DFPNISIRTCELALPFSAVMGIDKIRDLILRATEPQMVLFNLY----DDWLQETS 1957
Query: 753 SFGPVDKLDTRIFLTGPKVGEE 774
S+ +L + L V EE
Sbjct: 1958 SYTAFSRL--LLVLRALDVNEE 1977
>gnl|CDD|236454 PRK09288, purT, phosphoribosylglycinamide formyltransferase 2;
Validated.
Length = 395
Score = 29.7 bits (68), Expect = 9.8
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 103 TTTEEAMEFCLKYGLPVIFKAAYGGGGRGMRVVRKMEDVEENFQRASSEAKAAFGNGAMF 162
+ EE + G P + K G+G VVR ED+E+ ++ A + G G +
Sbjct: 136 DSLEELRAAVEEIGYPCVVKPVMSSSGKGQSVVRSPEDIEKAWEYAQEGGRG--GAGRVI 193
Query: 163 IEKFIE 168
+E+FI+
Sbjct: 194 VEEFID 199
>gnl|CDD|132460 TIGR03419, NifU_clost, FeS cluster assembly scaffold protein NifU,
Clostridium type. NifU and NifS form a pair of
iron-sulfur (FeS) cluster biosynthesis proteins much
simpler than the ISC and SUF systems. Members of this
protein family are a distinct group of NifU-like
proteins, found always to a NifS-like protein and
restricted to species that lack a SUF system. Typically,
NIF systems service a smaller number of FeS-containing
proteins than do ISC or SUF. Members of this particular
branch typically are found, almost half the time, near
the mnmA gene, involved in the carboxymethylaminomethyl
modification of U34 in some tRNAs (see GenProp0704).
While other NifU proteins are associated with nitrogen
fixation, this family is not [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 121
Score = 28.2 bits (63), Expect = 9.9
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 10/48 (20%)
Query: 915 GQVGAPMPGSVMEIRVKV-GDKVEK--------GAALVVLSAMKMEMV 953
G+VG P G +M+I +KV D ++ GAA + S+M EM+
Sbjct: 25 GEVGNPKCGDIMKIFLKVEDDIIKDVKFKTFGCGAA-IASSSMATEMI 71
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.393
Gapped
Lambda K H
0.267 0.0887 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 56,195,267
Number of extensions: 5755640
Number of successful extensions: 6888
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6713
Number of HSP's successfully gapped: 272
Length of query: 1080
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 973
Effective length of database: 6,191,724
Effective search space: 6024547452
Effective search space used: 6024547452
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 64 (28.1 bits)