RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13907
(698 letters)
>gnl|CDD|181899 PRK09485, mmuM, homocysteine methyltransferase; Provisional.
Length = 304
Score = 305 bits (783), Expect = 1e-98
Identities = 125/315 (39%), Positives = 177/315 (56%), Gaps = 20/315 (6%)
Query: 267 KINEFILENKLYLIDGGFSSQLSKHVGEDNVTEKDNPLWCSAFLHSNRQAVIDTHRDYVR 326
E + + + ++DG +++L G D ++ LW + L N + + H DY R
Sbjct: 3 PFKELLAQGPVLILDGALATELEAR-GCD----LNDSLWSAKVLLENPELIYQVHLDYFR 57
Query: 327 AGCDIVTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIALEEKRDPAIASRHVR 386
AG D T +YQA+ +GF GLSE ++ +LIR +V+ KEA RD A + +
Sbjct: 58 AGADCAITASYQATFQGFAAR-GLSEAEAEELIRRSVELAKEA------RDEFWAEKPL- 109
Query: 387 VAGSLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEE 446
VAGS+G YGA+L DGSEYRGDY + +EL D+HRPRIEAL + G DLLA ET+P +E
Sbjct: 110 VAGSVGPYGAYLADGSEYRGDY--GLSEEELQDFHRPRIEALAEAGADLLACETIPNLDE 167
Query: 447 AMVLAELIK-EYPGLKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLVAVGVNCLAP 505
A L EL+K E+PG+ AW+SF+ +D H G A + A +P Q+VAVGVNC AP
Sbjct: 168 AEALVELLKEEFPGVPAWLSFTLRDGTHISDGTPLAEAAA-LLAASP-QVVAVGVNCTAP 225
Query: 506 HYVESLLTSAGR--DVPLLCCPNSGETFDPGQRIWMNKDSVPSVDTYVPRWLDTGVKYVG 563
V + + + D PL+ PNSGE +D + W S+ P W G + +G
Sbjct: 226 ELVTAAIAALRAVTDKPLVVYPNSGEVYDAVTKTWHGPADDASLGELAPEWYAAGARLIG 285
Query: 564 GCCRTNADDMKNVNQ 578
GCCRT +D+ +
Sbjct: 286 GCCRTTPEDIAALAA 300
Score = 195 bits (498), Expect = 5e-57
Identities = 84/178 (47%), Positives = 113/178 (63%), Gaps = 13/178 (7%)
Query: 1 ASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIVLEEKRDPAIASRHVRVAGSLGSYGAFL 60
A+ +GF GLSE ++ +LIR +V+ KEA RD A + + VAGS+G YGA+L
Sbjct: 70 ATFQGFAAR-GLSEAEAEELIRRSVELAKEA------RDEFWAEKPL-VAGSVGPYGAYL 121
Query: 61 HDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEEAMVLAELIK-EY 119
DGSEYRGDY + +EL D+HRPRIEAL + G DLLA ET+P +EA L EL+K E+
Sbjct: 122 ADGSEYRGDY--GLSEEELQDFHRPRIEALAEAGADLLACETIPNLDEAEALVELLKEEF 179
Query: 120 PGLKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLVAVGVNCLAPHYVESLLTSA 177
PG+ AW+SF+ +D H G A + A +P Q+VAVGVNC AP V + + +
Sbjct: 180 PGVPAWLSFTLRDGTHISDGTPLAEAAA-LLAASP-QVVAVGVNCTAPELVTAAIAAL 235
>gnl|CDD|215269 PLN02489, PLN02489, homocysteine S-methyltransferase.
Length = 335
Score = 249 bits (639), Expect = 5e-77
Identities = 115/303 (37%), Positives = 174/303 (57%), Gaps = 22/303 (7%)
Query: 280 IDGGFSSQLSKHVGEDNVTEKDNPLWCSAFLHSNRQAVIDTHRDYVRAGCDIVTTNTYQA 339
IDGGF+++L +H + N +PLW + L ++ + H DY+ AG DI+ T +YQA
Sbjct: 25 IDGGFATELERHGADLN-----DPLWSAKCLITSPHLIRKVHLDYLEAGADIIITASYQA 79
Query: 340 SVEGFVQHLGLSEDQSVQLIRDAVKYVKEA--IALEE-------KRDPAIASRHVRVAGS 390
+++GF GLS ++S L+R +V+ EA I ++ + ++ R + VA S
Sbjct: 80 TIQGFESR-GLSREESETLLRKSVEIACEARDIFWDKCQKGSTSRPGRELSYRPILVAAS 138
Query: 391 LGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEEAMVL 450
+GSYGA+L DGSEY GDY S T ++L D+HR R++ L + G DL+A ET+P + EA
Sbjct: 139 IGSYGAYLADGSEYSGDYGPSVTLEKLKDFHRRRLQVLAEAGPDLIAFETIPNKLEAQAY 198
Query: 451 AELIKEYPG-LKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLVAVGVNCLAPHYVE 509
EL++E + AWISF+ KD + GD A A + ++VAVG+NC P ++
Sbjct: 199 VELLEEENIKIPAWISFNSKDGVNVVSGDSLLECAS--IADSCKKVVAVGINCTPPRFIH 256
Query: 510 SLLTSAGRDV--PLLCCPNSGETFDPGQRIWMNKDSVPSVD--TYVPRWLDTGVKYVGGC 565
L+ S + P++ PNSGET+D + W+ V D +YV +W D G +GGC
Sbjct: 257 GLILSIRKVTSKPIVVYPNSGETYDGEAKEWVESTGVSDEDFVSYVNKWRDAGASLIGGC 316
Query: 566 CRT 568
CRT
Sbjct: 317 CRT 319
Score = 156 bits (397), Expect = 2e-42
Identities = 71/188 (37%), Positives = 108/188 (57%), Gaps = 13/188 (6%)
Query: 1 ASVEGFVQHLGLSEDQSVQLIRDAVKYVKEA--IVLEE-------KRDPAIASRHVRVAG 51
A+++GF GLS ++S L+R +V+ EA I ++ + ++ R + VA
Sbjct: 79 ATIQGFESR-GLSREESETLLRKSVEIACEARDIFWDKCQKGSTSRPGRELSYRPILVAA 137
Query: 52 SLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEEAMV 111
S+GSYGA+L DGSEY GDY S T ++L D+HR R++ L + G DL+A ET+P + EA
Sbjct: 138 SIGSYGAYLADGSEYSGDYGPSVTLEKLKDFHRRRLQVLAEAGPDLIAFETIPNKLEAQA 197
Query: 112 LAELIKEYPG-LKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLVAVGVNCLAPHYV 170
EL++E + AWISF+ KD + GD A A + ++VAVG+NC P ++
Sbjct: 198 YVELLEEENIKIPAWISFNSKDGVNVVSGDSLLECAS--IADSCKKVVAVGINCTPPRFI 255
Query: 171 ESLLTSAE 178
L+ S
Sbjct: 256 HGLILSIR 263
>gnl|CDD|224951 COG2040, MHT1, Homocysteine/selenocysteine methylase
(S-methylmethionine-dependent) [Amino acid transport and
metabolism].
Length = 300
Score = 211 bits (540), Expect = 4e-63
Identities = 111/309 (35%), Positives = 160/309 (51%), Gaps = 25/309 (8%)
Query: 268 INEFILENKLYLIDGGFSSQLSKHVGEDNVTEKDNPLWCSAFLHSNRQAVIDTHRDYVRA 327
I + + ++DGG +++L + G D +PLW + L + V + H D++RA
Sbjct: 1 IKHELDTLSVLILDGGLATELERR-GCD----LSDPLWSALALVDEPEIVRNVHADFLRA 55
Query: 328 GCDIVTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIALEEKRDPAIASRHVRV 387
G DI+TT TYQA+ EGF + +SED++ QLIR +V+ + A RD A + +
Sbjct: 56 GADIITTATYQATPEGFAER--VSEDEAKQLIRRSVELARAA------RD-AYGEENQNI 106
Query: 388 AGSLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEEA 447
AGSLG YGA L D EYRGDY + L +HRPRIEAL + G DLLA ETLP EA
Sbjct: 107 AGSLGPYGAALAD--EYRGDY--GASQDALYKFHRPRIEALNEAGADLLACETLPNITEA 162
Query: 448 MVLAELIKEYPGLKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLVAVGVNCLAPHY 507
+ +L++E+ AWISF+ D+ G A + A+GVNC P +
Sbjct: 163 EAIVQLVQEF-SKPAWISFTLNDDTRLRDGTPLSEAA--AILAGLPNIAALGVNCCHPDH 219
Query: 508 VESLLTS---AGRDVPLLCCPNSGETFDPGQRIWMNKDSVP-SVDTYVPRWLDTGVKYVG 563
+ + + P++ PNSGE +DP + W S T W++ G + +G
Sbjct: 220 IPAAIEELSKLLTGKPIIVYPNSGEQYDPAGKTWHGPALSADSYSTLAKSWVEAGARIIG 279
Query: 564 GCCRTNADD 572
GCCRT
Sbjct: 280 GCCRTGPAH 288
Score = 115 bits (290), Expect = 2e-28
Identities = 69/189 (36%), Positives = 96/189 (50%), Gaps = 16/189 (8%)
Query: 1 ASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIVLEEKRDPAIASRHVRVAGSLGSYGAFL 60
A+ EGF + + SED++ QLIR +V+ + A RD A + +AGSLG YGA L
Sbjct: 67 ATPEGFAERV--SEDEAKQLIRRSVELARAA------RD-AYGEENQNIAGSLGPYGAAL 117
Query: 61 HDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEEAMVLAELIKEYP 120
D EYRGDY + L +HRPRIEAL + G DLLA ETLP EA + +L++E+
Sbjct: 118 AD--EYRGDY--GASQDALYKFHRPRIEALNEAGADLLACETLPNITEAEAIVQLVQEF- 172
Query: 121 GLKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLVAVGVNCLAPHYVESLLTSAEVE 180
AWISF+ D+ G A + A+GVNC P ++ + +
Sbjct: 173 SKPAWISFTLNDDTRLRDGTPLSEAA--AILAGLPNIAALGVNCCHPDHIPAAIEELSKL 230
Query: 181 GQSLELPVN 189
+ V
Sbjct: 231 LTGKPIIVY 239
>gnl|CDD|217114 pfam02574, S-methyl_trans, Homocysteine S-methyltransferase. This
is a family of related homocysteine S-methyltransferases
enzymes: 5-methyltetrahydrofolate--homocysteine
S-methyltransferases also known EC:2.1.1.13;
Betaine--homocysteine S-methyltransferase (vitamin B12
dependent), EC:2.1.1.5; and Homocysteine
S-methyltransferase, EC:2.1.1.10.
Length = 303
Score = 190 bits (485), Expect = 3e-55
Identities = 95/309 (30%), Positives = 142/309 (45%), Gaps = 29/309 (9%)
Query: 279 LIDGGFSSQLSKHVGEDNVTEKDNPLWCSAF-----LHSNRQAVIDTHRDYVRAGCDIVT 333
++DGG ++L + +PLW S + + + + H+ Y+ AG DI+
Sbjct: 3 VLDGGMGTEL-----QRRGLNLADPLW-SEGCNEELSITKPELIREIHKAYLEAGADIIE 56
Query: 334 TNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIALEEKRDPAIASRHVRVAGSLGS 393
TNTYQA+ GF + GL + +L R A + + A + VAGS+G
Sbjct: 57 TNTYQATPIGFADY-GLEHLELRELNRRAAEIARAA-----ADEYGNTGDKRLVAGSIGP 110
Query: 394 YGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEEAMVLAEL 453
YGA DGSEY G Y + +EL HRP++E L+ GG+DLL +ET+P EA
Sbjct: 111 YGAT-ADGSEYPGYY--GVSFEELKKAHRPQLEGLLDGGVDLLLLETIPDFLEAKAAVRA 167
Query: 454 IKEYPGLKAWISFSCKDEKHTCHGDKFGLIAR---DVYAKNPAQLVAVGVNCLAPHYVES 510
++E WISF D G L A++ AVGVNC +
Sbjct: 168 VEEVFEAPGWISFPVFDSGTLVDGTGLTLSGATIEAALNSVQAEIDAVGVNCALGPDIMD 227
Query: 511 L---LTSAGRDVPLLCCPNSGETFDPGQRIW--MNKDSVPSVDTYVPRWLDTGVKYVGGC 565
L S PL PNSGE +D G++ + + PS + ++ +G + +GGC
Sbjct: 228 EILELLSLTARKPLSVYPNSGEPYDAGKKEYDGTPDELAPSY-WSLKEFVASGARIIGGC 286
Query: 566 CRTNADDMK 574
C T D ++
Sbjct: 287 CGTTPDHIR 295
Score = 106 bits (266), Expect = 3e-25
Identities = 55/173 (31%), Positives = 74/173 (42%), Gaps = 18/173 (10%)
Query: 1 ASVEGFVQHLGLSEDQSVQLIRDAVKY---VKEAIVLEEKRDPAIASRHVRVAGSLGSYG 57
A+ GF + GL + +L R A + + VAGS+G YG
Sbjct: 62 ATPIGFADY-GLEHLELRELNRRAAEIARAAADEYGNT--------GDKRLVAGSIGPYG 112
Query: 58 AFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEEAMVLAELIK 117
A DGSEY G Y + +EL HRP++E L+ GG+DLL +ET+P EA ++
Sbjct: 113 AT-ADGSEYPGYY--GVSFEELKKAHRPQLEGLLDGGVDLLLLETIPDFLEAKAAVRAVE 169
Query: 118 EYPGLKAWISFSCKDEKHTCHGDKFGLIAR---DVYAKNPAQLVAVGVNCLAP 167
E WISF D G L A++ AVGVNC
Sbjct: 170 EVFEAPGWISFPVFDSGTLVDGTGLTLSGATIEAALNSVQAEIDAVGVNCALG 222
>gnl|CDD|146336 pfam03643, Vps26, Vacuolar protein sorting-associated protein 26.
Vacuolar protein sorting-associated protein (Vps) 26 is
one of around 50 proteins involved in protein
trafficking. In particular, Vps26 assembles into a
retromer complex with at least four other proteins Vps5,
Vps17, Vps29 and Vps35. This family also contains Down
syndrome critical region 3/A.
Length = 275
Score = 89.8 bits (223), Expect = 7e-20
Identities = 28/125 (22%), Positives = 47/125 (37%), Gaps = 23/125 (18%)
Query: 583 FSITPESLTNARDK------------FNIPRFRISGHLDSTECSVVRPFTGEIVIEQTEL 630
F+ PE+ + + + +N ++ HL G+I +
Sbjct: 146 FTTYPETNNSIKMEVGIEDCLHIEFEYNKSKY----HLKDV-------IVGKIYFLLVRI 194
Query: 631 PIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVFPRLFTCPTLI 690
IK +ELQL+R E+ G ++ I +I +G G IPI + PT+
Sbjct: 195 KIKHMELQLIRRESTGTGPNTFTESETIAKFEIMDGAPVRGESIPIRLFLAGYDLTPTMR 254
Query: 691 TSNFK 695
N K
Sbjct: 255 DVNKK 259
Score = 63.2 bits (154), Expect = 7e-11
Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 10/80 (12%)
Query: 196 KPIQLLSIELELAAAGKMPSGTTQIPFEAPLKAKPNRSLFETYHGVFVNVQYNLKCELKR 255
P + ++ ELA G++ T PFE PL KP +E+Y GV V ++Y L+ + R
Sbjct: 76 NPHEFTNLVRELAPPGELTQSKT-FPFEFPLVEKP----YESYIGVNVRLRYFLRVTVVR 130
Query: 256 SHFNILSKDLQKINEFILEN 275
D+ K +F + N
Sbjct: 131 R-----LTDITKEKDFWVHN 145
>gnl|CDD|236321 PRK08645, PRK08645, bifunctional homocysteine
S-methyltransferase/5,10-methylenetetrahydrofolate
reductase protein; Reviewed.
Length = 612
Score = 91.4 bits (228), Expect = 4e-19
Identities = 74/270 (27%), Positives = 127/270 (47%), Gaps = 49/270 (18%)
Query: 312 SNRQAVIDTHRDYVRAGCDIVTTNTYQA---SVEGFVQHLGLSEDQSVQLIRDAVKYVKE 368
S+ + ++ HR+Y+ AG D++ TNT+ A ++ + GL ED+ ++ R AV+ +E
Sbjct: 40 SHPELILRIHREYIEAGADVIQTNTFGANRIKLKRY----GL-EDKVKEINRAAVRLARE 94
Query: 369 AIALEEKRDPAIASRHVRVAGSLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEAL 428
A A V VAG++G G RG D + +E+ R +I+AL
Sbjct: 95 A-----------AGDDVYVAGTIGPIGG--------RGPLGD-ISLEEIRREFREQIDAL 134
Query: 429 IQGGIDLLAIETLPAQEEAMVLAELIKEYPGLKAWISFSCKDEKHTCHGDKFGLIARDVY 488
++ G+D L +ET EE ++ E +E L + ++ T + G +
Sbjct: 135 LEEGVDGLLLETFYDLEELLLALEAAREKTDLPIIAQVAFHEDGVT----QNGTSLEEAL 190
Query: 489 AKNPAQLVA-----VGVNC-LAPHYV-ESLLT-SAGRDVPLLCCPNSG--ETFDPGQRIW 538
+LVA VG+NC L P+++ E+L + PL PN+G E D G+ ++
Sbjct: 191 ----KELVAAGADVVGLNCGLGPYHMLEALERIPIPENAPLSAYPNAGLPEYVD-GRYVY 245
Query: 539 MNKDSVPSVDTYVPRWLDTGVKYVGGCCRT 568
+ Y +++ GV+ +GGCC T
Sbjct: 246 S--ANPEYFAEYALEFVEQGVRLIGGCCGT 273
Score = 43.7 bits (104), Expect = 3e-04
Identities = 44/172 (25%), Positives = 74/172 (43%), Gaps = 34/172 (19%)
Query: 14 EDQSVQLIRDAVKYVKEAIVLEEKRDPAIASRHVRVAGSLGSYGAFLHDGSEYRGDYIDS 73
ED+ ++ R AV+ +EA A V VAG++G G RG D
Sbjct: 78 EDKVKEINRAAVRLAREA-----------AGDDVYVAGTIGPIGG--------RGPLGD- 117
Query: 74 TTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEEAMVLAELIKEYPGLKAWISFSCKDE 133
+ +E+ R +I+AL++ G+D L +ET EE ++ E +E L + ++
Sbjct: 118 ISLEEIRREFREQIDALLEEGVDGLLLETFYDLEELLLALEAAREKTDLPIIAQVAFHED 177
Query: 134 KHTCHGDKFGLIARDVYAKNPAQLVA-----VGVNC-LAPHYVESLLTSAEV 179
T + G + +LVA VG+NC L P+++ L +
Sbjct: 178 GVT----QNGTSLEEAL----KELVAAGADVVGLNCGLGPYHMLEALERIPI 221
>gnl|CDD|223719 COG0646, MetH, Methionine synthase I (cobalamin-dependent),
methyltransferase domain [Amino acid transport and
metabolism].
Length = 311
Score = 82.0 bits (203), Expect = 7e-17
Identities = 77/308 (25%), Positives = 123/308 (39%), Gaps = 34/308 (11%)
Query: 273 LENKLYLIDGGFSSQLSK---HVGEDNVTEKDNPLWCSAFLHSNRQAVIDTHRDYVRAGC 329
L+ ++ ++DG + L + + +N L + + HR Y+ AG
Sbjct: 12 LKERVLVLDGAMGTMLQSYGLDEADFRGLKGNNELLN----LTKPDVIEAIHRAYIEAGA 67
Query: 330 DIVTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIALEEKRDPAIASRHVRVAG 389
DI+ TNT+ A+ + GL ED+ ++ + A + + A P VAG
Sbjct: 68 DIIETNTFGATTIKLADY-GL-EDKVYEINQKAARIARRAADEAGDPKPRF------VAG 119
Query: 390 SLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEEAMV 449
S+G L D+ + T EL++ +R ++E LI GG DL+ IET+ A
Sbjct: 120 SIGPTNKTL----SISPDF--AVTFDELVEAYREQVEGLIDGGADLILIETIFDTLNAKA 173
Query: 450 LAELIKE-----YPGLKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLVAVGVNC-L 503
+E L IS + D T G + P AVG+NC L
Sbjct: 174 AVFAAREVFEELGVRLPVMISGTITDSGRTLSGQTIEAFLNSLEHLGP---DAVGLNCAL 230
Query: 504 APHYVESLL--TSAGRDVPLLCCPNSGETFDPGQRIWMNKDSVPSVDTYVPRW-LDTGVK 560
P + L S D + PN+G G+R + + + + + + GV
Sbjct: 231 GPDEMRPHLRELSRIADAFVSVYPNAGLPNAFGERAVYD-LTPEYMAEALAEFAEEGGVN 289
Query: 561 YVGGCCRT 568
VGGCC T
Sbjct: 290 IVGGCCGT 297
Score = 44.6 bits (106), Expect = 1e-04
Identities = 41/156 (26%), Positives = 62/156 (39%), Gaps = 20/156 (12%)
Query: 14 EDQSVQLIRDAVKYVKEAIVLEEKRDPAIASRHVRVAGSLGSYGAFLHDGSEYRGDYIDS 73
ED+ ++ + A + + A D A + VAGS+G L D+ +
Sbjct: 88 EDKVYEINQKAARIARRAA------DEAGDPKPRFVAGSIGPTNKTL----SISPDF--A 135
Query: 74 TTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEEAMVLAELIKE-----YPGLKAWISF 128
T EL++ +R ++E LI GG DL+ IET+ A +E L IS
Sbjct: 136 VTFDELVEAYREQVEGLIDGGADLILIETIFDTLNAKAAVFAAREVFEELGVRLPVMISG 195
Query: 129 SCKDEKHTCHGDKFGLIARDVYAKNPAQLVAVGVNC 164
+ D T G + P AVG+NC
Sbjct: 196 TITDSGRTLSGQTIEAFLNSLEHLGP---DAVGLNC 228
>gnl|CDD|233714 TIGR02082, metH, 5-methyltetrahydrofolate--homocysteine
methyltransferase. This family represents
5-methyltetrahydrofolate--homocysteine methyltransferase
(EC 2.1.1.13), one of at least three different enzymes
able to convert homocysteine to methionine by
transferring a methyl group on to the sulfur atom. It is
also called the vitamin B12(or cobalamine)-dependent
methionine synthase. Other methionine synthases include
5-methyltetrahydropteroyltriglutamate--homocysteine
S-methyltransferase (MetE, EC 2.1.1.14, the
cobalamin-independent methionine synthase) and
betaine-homocysteine methyltransferase [Amino acid
biosynthesis, Aspartate family].
Length = 1178
Score = 64.0 bits (156), Expect = 2e-10
Identities = 77/334 (23%), Positives = 125/334 (37%), Gaps = 50/334 (14%)
Query: 273 LENKLYLIDGGFSSQLSKHVGEDNVTEKD----------NPLWCSAFLHSNRQAVIDT-H 321
L ++ ++DG +QL N+TE D + L+ + VI T H
Sbjct: 1 LNQRILVLDGAMGTQLQSA----NLTEADFRGAEFTCHRELKGNNDILNLTKPEVIATIH 56
Query: 322 RDYVRAGCDIVTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIALEEKRDPAIA 381
R Y AG DI+ TNT+ ++ Q ED L K +
Sbjct: 57 RAYFEAGADIIETNTFNSTT--ISQADYDLEDLIYDLNFKGAKLARAVADEFTLTP---- 110
Query: 382 SRHVRVAGSLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETL 441
+ VAGS+G + + T EL+D + + + L+ GG+DLL IET
Sbjct: 111 EKPRFVAGSMGPTNKTATLSPDVERPGFRNVTYDELVDAYTEQAKGLLDGGVDLLLIETC 170
Query: 442 --PAQEEAMVLA---ELIKEYPGLKAWISFSCKDEK-HTCHGDKFGLIARDVYAKNPAQL 495
+A + A ++ L IS + D T G + A +
Sbjct: 171 FDTLNAKAALFAAETVFEEKGRELPIMISGTIVDTSGRTLSGQTIEAFLTSL---EHAGI 227
Query: 496 VAVGVNC------LAPHYVESLLTSAGRDVPLLCCPNSG--ETFDPGQRIWMNKDSVPS- 546
+G+NC + PH ++ L S + + C PN+G F D P
Sbjct: 228 DMIGLNCALGPDEMRPH-LKHL--SEHAEAYVSCHPNAGLPNAFG-------EYDLTPDE 277
Query: 547 VDTYVPRW-LDTGVKYVGGCCRTNADDMKNVNQV 579
+ + + + G+ VGGCC T D ++ + +
Sbjct: 278 LAKALADFAAEGGLNIVGGCCGTTPDHIRAIAEA 311
Score = 35.5 bits (82), Expect = 0.10
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 49 VAGSLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETL--PAQ 106
VAGS+G + + T EL+D + + + L+ GG+DLL IET
Sbjct: 116 VAGSMGPTNKTATLSPDVERPGFRNVTYDELVDAYTEQAKGLLDGGVDLLLIETCFDTLN 175
Query: 107 EEAMVLA 113
+A + A
Sbjct: 176 AKAALFA 182
>gnl|CDD|236045 PRK07534, PRK07534, methionine synthase I; Validated.
Length = 336
Score = 56.7 bits (137), Expect = 2e-08
Identities = 68/265 (25%), Positives = 106/265 (40%), Gaps = 51/265 (19%)
Query: 321 HRDYVRAGCDIVTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIALEEKRDPAI 380
H+ +V AG DI+ TN++ + H ++D+ +L R A + +E
Sbjct: 51 HQGFVDAGSDIILTNSFGGTAARLKLHD--AQDRVHELNRAAAEIAREVADK-------- 100
Query: 381 ASRHVRVAGSLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIET 440
A R V VAGS+G G + + + T ++ + E L GG D+L +ET
Sbjct: 101 AGRKVIVAGSVGPTGEIMEP--------MGALTHALAVEAFHEQAEGLKAGGADVLWVET 152
Query: 441 LPAQEEAMVLAELIKEYPGLKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQL----- 495
+ A EE AE K G+ W C F R + PA L
Sbjct: 153 ISAPEEIRAAAEAAKL-AGM-PW-----------CGTMSFDTAGRTMMGLTPADLADLVE 199
Query: 496 ------VAVGVNC--LAPHYVESLL--TSAGRDVPLLCCPNSG-ETFDPGQRIWMNKDSV 544
+A G NC A + ++L T+ G + P++ N+G + G + D
Sbjct: 200 KLGEPPLAFGANCGVGASDLLRTVLGFTAQGPERPIIAKGNAGIPKYVDGHIHY---DGT 256
Query: 545 PSV-DTYVPRWLDTGVKYVGGCCRT 568
P + Y D G + +GGCC T
Sbjct: 257 PELMAEYAVLARDAGARIIGGCCGT 281
Score = 37.8 bits (88), Expect = 0.016
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 8/72 (11%)
Query: 43 ASRHVRVAGSLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIET 102
A R V VAGS+G G + + + T ++ + E L GG D+L +ET
Sbjct: 101 AGRKVIVAGSVGPTGEIMEP--------MGALTHALAVEAFHEQAEGLKAGGADVLWVET 152
Query: 103 LPAQEEAMVLAE 114
+ A EE AE
Sbjct: 153 ISAPEEIRAAAE 164
>gnl|CDD|236539 PRK09490, metH, B12-dependent methionine synthase; Provisional.
Length = 1229
Score = 54.4 bits (132), Expect = 2e-07
Identities = 38/136 (27%), Positives = 59/136 (43%), Gaps = 25/136 (18%)
Query: 315 QAVIDTHRDYVRAGCDIVTTNTYQASVEGFVQHLGLS----EDQSVQLIRDAVKYVKEAI 370
+ HR Y+ AG DI+ TNT+ A+ + + E +L A + +EA
Sbjct: 65 DVIEAIHRAYLEAGADIIETNTFNATT------IAQADYGMESLVYELNFAAARLAREAA 118
Query: 371 ALEEKRDPAIASRHVRVAGSLG------SYGAFLHDGSEYRGDYIDSTTPQELIDYHRPR 424
+ P + VAG LG S ++D +R + T EL+ +R +
Sbjct: 119 DEWTAKTPD---KPRFVAGVLGPTNRTASISPDVND-PGFR-----NVTFDELVAAYREQ 169
Query: 425 IEALIQGGIDLLAIET 440
LI+GG DL+ IET
Sbjct: 170 TRGLIEGGADLILIET 185
Score = 33.2 bits (77), Expect = 0.53
Identities = 27/95 (28%), Positives = 41/95 (43%), Gaps = 15/95 (15%)
Query: 14 EDQSVQLIRDAVKYVKEAIVLEEKRDPAIASRHVRVAGSLG------SYGAFLHDGSEYR 67
E +L A + +EA + P + VAG LG S ++D +R
Sbjct: 100 ESLVYELNFAAARLAREAADEWTAKTPD---KPRFVAGVLGPTNRTASISPDVND-PGFR 155
Query: 68 GDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIET 102
+ T EL+ +R + LI+GG DL+ IET
Sbjct: 156 -----NVTFDELVAAYREQTRGLIEGGADLILIET 185
>gnl|CDD|216571 pfam01558, POR, Pyruvate ferredoxin/flavodoxin oxidoreductase.
This family includes a region of the large protein
pyruvate-flavodoxin oxidoreductase and the whole
pyruvate ferredoxin oxidoreductase gamma subunit
protein. It is not known whether the gamma subunit has a
catalytic or regulatory role. Pyruvate oxidoreductase
(POR) catalyzes the final step in the fermentation of
carbohydrates in anaerobic microorganisms. This involves
the oxidative decarboxylation of pyruvate with the
participation of thiamine followed by the transfer of an
acetyl moiety to coenzyme A for the synthesis of
acetyl-CoA. The family also includes pyruvate flavodoxin
oxidoreductase as encoded by the nifJ gene in
cyanobacterium which is required for growth on molecular
nitrogen when iron is limited.
Length = 129
Score = 31.0 bits (71), Expect = 0.87
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 315 QAVIDTHRDYVRAGCDIVTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIAL 372
+D H D ++ G I+ NT + LGL + + IR+ ++ I L
Sbjct: 66 PETLDRHLDGLKPGGIIIVANT--VMLGALAALLGLPLEALEEAIREQFGKKEKVIEL 121
>gnl|CDD|225911 COG3376, HoxN, High-affinity nickel permease [Inorganic ion
transport and metabolism].
Length = 342
Score = 31.5 bits (72), Expect = 1.3
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 655 ATEIQNIQIGEGNVFTGIPIPIYMVFPRLFT 685
ATEI + I + GIPI +VFP LF
Sbjct: 210 ATEIALLAISAASAAIGIPIYAILVFPILFA 240
>gnl|CDD|235873 PRK06846, PRK06846, putative deaminase; Validated.
Length = 410
Score = 31.5 bits (72), Expect = 1.5
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 13/52 (25%)
Query: 313 NRQAVIDTHRDYVRAGCDIVTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVK 364
N QA ++ ++D +IV F QH GL S L+R+A+K
Sbjct: 148 NLQAALERYKDGF--TYEIV----------AFPQH-GLLRSNSEPLMREAMK 186
>gnl|CDD|235360 PRK05183, hscA, chaperone protein HscA; Provisional.
Length = 616
Score = 31.7 bits (73), Expect = 1.6
Identities = 25/96 (26%), Positives = 44/96 (45%), Gaps = 21/96 (21%)
Query: 349 GLSEDQSVQLIRDAVKYVKEAI---ALEEKRDPAIASRHVRVAGSLGSYGAFLHDGSEYR 405
GL++D+ ++++D++ + +E + AL E++ A RV +L + A DG
Sbjct: 503 GLTDDEIARMLKDSMSHAEEDMQARALAEQKVEA-----ERVLEALQA--ALAADG---- 551
Query: 406 GDYIDSTTPQEL--IDYHRPRIEALIQGGIDLLAIE 439
D + E ID + + QG D AIE
Sbjct: 552 ----DLLSAAERAAIDAAMAALREVAQGD-DADAIE 582
Score = 30.9 bits (71), Expect = 2.9
Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 21/96 (21%)
Query: 11 GLSEDQSVQLIRDAVKYVKEAI---VLEEKRDPAIASRHVRVAGSLGSYGAFLHDGSEYR 67
GL++D+ ++++D++ + +E + L E++ A RV +L + A DG
Sbjct: 503 GLTDDEIARMLKDSMSHAEEDMQARALAEQKVEA-----ERVLEALQA--ALAADG---- 551
Query: 68 GDYIDSTTPQEL--IDYHRPRIEALIQGGIDLLAIE 101
D + E ID + + QG D AIE
Sbjct: 552 ----DLLSAAERAAIDAAMAALREVAQGD-DADAIE 582
>gnl|CDD|188632 cd00452, KDPG_aldolase, KDPG and KHG aldolase. KDPG and KHG
aldolase. This family belongs to the class I adolases
whose reaction mechanism involves Schiff base formation
between a substrate carbonyl and lysine residue in the
active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG)
aldolase, is best known for its role in the
Entner-Doudoroff pathway of bacteria, where it catalyzes
the reversible cleavage of KDPG to pyruvate and
glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate
(KHG) aldolase, which has enzymatic specificity toward
glyoxylate, forming KHG in the presence of pyruvate, and
is capable of regulating glyoxylate levels in the
glyoxylate bypass, an alternate pathway when bacteria
are grown on acetate carbon sources.
Length = 190
Score = 30.2 bits (69), Expect = 2.6
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 85 PRIEALIQGGIDLLAIETLPAQEEAMVLAELIKEYPGL 122
EALI+GGI + I TL + L KE+P
Sbjct: 20 ALAEALIEGGIRAIEI-TLRTPGALEAIRALRKEFPEA 56
Score = 30.2 bits (69), Expect = 2.6
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 423 PRIEALIQGGIDLLAIETLPAQEEAMVLAELIKEYPGL 460
EALI+GGI + I TL + L KE+P
Sbjct: 20 ALAEALIEGGIRAIEI-TLRTPGALEAIRALRKEFPEA 56
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 29.9 bits (67), Expect = 3.5
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 12/73 (16%)
Query: 141 KFGLIARDVYAKNPAQLVA---VGVNCLAPHYVESLLTSAEVEGQSLELPVNNTLISRKP 197
K G+I ++K+ AQ +A V VNC+AP ++ES +T + Q ++ P
Sbjct: 156 KAGMIG---FSKSLAQEIATRNVTVNCVAPGFIESAMTGKLNDKQ------KEAIMGAIP 206
Query: 198 IQLLSIELELAAA 210
++ + E+A+A
Sbjct: 207 MKRMGTGAEVASA 219
Score = 29.9 bits (67), Expect = 3.6
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 6/38 (15%)
Query: 479 KFGLIARDVYAKNPAQLVA---VGVNCLAPHYVESLLT 513
K G+I ++K+ AQ +A V VNC+AP ++ES +T
Sbjct: 156 KAGMIG---FSKSLAQEIATRNVTVNCVAPGFIESAMT 190
>gnl|CDD|217985 pfam04245, NA37, 37-kD nucleoid-associated bacterial protein.
Length = 320
Score = 29.6 bits (67), Expect = 5.5
Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 13/76 (17%)
Query: 308 AFLHSNRQAVIDTHRDYVRA--GCDIV-----TTNTYQASVEGFVQHLGLSEDQSVQLIR 360
+F+ + D+ GCD T +VE F + + L +++ ++
Sbjct: 158 SFIDGRGKRA----SDFFEDFLGCDEGVDAKEQTKKLLKAVEDFAKSVELDKEEKEEVRN 213
Query: 361 DAVKYVK--EAIALEE 374
V Y+K E I LEE
Sbjct: 214 KVVDYLKEGEEINLEE 229
>gnl|CDD|215866 pfam00339, Arrestin_N, Arrestin (or S-antigen), N-terminal domain.
Ig-like beta-sandwich fold. Scop reports duplication
with C-terminal domain.
Length = 148
Score = 28.8 bits (65), Expect = 5.6
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 8/60 (13%)
Query: 212 KMPSGTTQIPFEAPLKAKPNRSLFETYHGVFVNVQYNLKCELKRSHFNILSKDLQKINEF 271
++P+GT PF L S FE G ++Y +K EL R KD ++ F
Sbjct: 88 ELPAGTHAFPFSFELPPNCPPS-FEGQPG---GIRYEVKVELDRPW----KKDHKRKKVF 139
>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
Length = 373
Score = 29.7 bits (67), Expect = 5.9
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 105 AQEEAMVLAELIKEYPGLKAWISFSCKDEKHT 136
A E+A+VLA + Y KA + KHT
Sbjct: 293 AMEDAIVLANCLNAYDFEKALQRYDKIRVKHT 324
Score = 29.7 bits (67), Expect = 5.9
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 443 AQEEAMVLAELIKEYPGLKAWISFSCKDEKHT 474
A E+A+VLA + Y KA + KHT
Sbjct: 293 AMEDAIVLANCLNAYDFEKALQRYDKIRVKHT 324
>gnl|CDD|220809 pfam10561, UPF0565, Uncharacterized protein family UPF0565. This
family of proteins has no known function.
Length = 295
Score = 29.0 bits (65), Expect = 8.8
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 4/71 (5%)
Query: 258 FNILSKDLQKINEFILEN--KLYLIDGGFSSQLSKHVGEDNVTEKDNPLWCSAFLHSNRQ 315
+ L D E L + +Y +DGG + + + NV E+ + +H
Sbjct: 210 LHYLKIDTSI--ESFLSSISDMYWLDGGHNGGSYTWITDKNVLEELSQRGLKIHVHVTPY 267
Query: 316 AVIDTHRDYVR 326
V D R ++R
Sbjct: 268 QVRDPMRPWIR 278
>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517). This
family consists of several hypothetical glycine rich
plant and bacterial proteins of around 300 residues in
length. The function of this family is unknown.
Length = 280
Score = 28.8 bits (65), Expect = 9.3
Identities = 20/44 (45%), Positives = 25/44 (56%), Gaps = 9/44 (20%)
Query: 88 EALIQ-GGI---DLLAIETL--PAQEEAMVLA--ELIKEYPGLK 123
EAL G I DLLA+E L P Q E L+ EL+ +YP L+
Sbjct: 236 EALRILGSIPSDDLLAVEVLWTP-QGEGDTLSEDELLTDYPNLR 278
Score = 28.8 bits (65), Expect = 9.3
Identities = 20/44 (45%), Positives = 25/44 (56%), Gaps = 9/44 (20%)
Query: 426 EALIQ-GGI---DLLAIETL--PAQEEAMVLA--ELIKEYPGLK 461
EAL G I DLLA+E L P Q E L+ EL+ +YP L+
Sbjct: 236 EALRILGSIPSDDLLAVEVLWTP-QGEGDTLSEDELLTDYPNLR 278
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of
this protein are restricted to the Gram-positive
lineages, including the Mycoplasmas. This protein is
designated alpha chain and given the gene symbol polC,
but is not a full-length homolog of other polC genes.
The N-terminal region of about 200 amino acids is rich
in low-complexity sequence, poorly alignable, and not
included n this model [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1213
Score = 29.3 bits (66), Expect = 9.7
Identities = 19/66 (28%), Positives = 23/66 (34%), Gaps = 17/66 (25%)
Query: 500 VNCLAPHY----------VESLLTSAGRDVPLLCCPNSGETFDP-GQRI------WMNKD 542
VN L PHY + +G D+P CP G GQ I D
Sbjct: 677 VNPLPPHYLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPLKKDGQDIPFETFLGFKGD 736
Query: 543 SVPSVD 548
VP +D
Sbjct: 737 KVPDID 742
>gnl|CDD|218431 pfam05099, TerB, Tellurite resistance protein TerB. This family
contains the TerB tellurite resistance proteins from a a
number of bacteria.
Length = 140
Score = 27.9 bits (63), Expect = 9.8
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 344 FVQHLGLSEDQSVQLIRDAVKYVKEAIALEE 374
GL +++ LI A + +EA L E
Sbjct: 52 LRSRFGLDPEEAAALIELAEEAEQEAPDLYE 82
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 0.404
Gapped
Lambda K H
0.267 0.0886 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 35,847,913
Number of extensions: 3585063
Number of successful extensions: 3493
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3442
Number of HSP's successfully gapped: 51
Length of query: 698
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 594
Effective length of database: 6,324,786
Effective search space: 3756922884
Effective search space used: 3756922884
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: 62 (27.4 bits)