RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7967
(353 letters)
>gnl|CDD|216402 pfam01268, FTHFS, Formate--tetrahydrofolate ligase.
Length = 557
Score = 280 bits (720), Expect = 3e-90
Identities = 98/149 (65%), Positives = 114/149 (76%), Gaps = 11/149 (7%)
Query: 55 GLTGAMAVLLKDAVQPNLMQTLEGTPVMVHAGPFANIAHGCSSVVADLIALKLVGAEGYV 114
G+ GAM LLKDA++PNL+QTLEGTP +VH GPFANIAHGC+S++A IALKL YV
Sbjct: 239 GVAGAMTALLKDAIKPNLVQTLEGTPALVHGGPFANIAHGCNSIIATKIALKLA---DYV 295
Query: 115 VTEAGFGSDIGMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTE 174
VTEAGFG+D+G EKFF+IKCR SG PDAVVLV TVRALKMHGG K + TE
Sbjct: 296 VTEAGFGADLGAEKFFDIKCRKSGLKPDAVVLVATVRALKMHGGVA--------KDDLTE 347
Query: 175 ENLDLVQKGCVNLEKHVSNGLKFGVPVVV 203
ENL+ ++KG NLEKH+ N KFGVPVVV
Sbjct: 348 ENLEALEKGFANLEKHIENVKKFGVPVVV 376
Score = 112 bits (282), Expect = 3e-27
Identities = 38/93 (40%), Positives = 51/93 (54%), Gaps = 15/93 (16%)
Query: 240 RLNINPDTISWRRV-------------GQSPTEKNMERSTGFDISVASEVMAALALSKNL 286
L+I+P I+W+RV G + R GFDI+VASE+MA L L+ +L
Sbjct: 153 ELDIDPRRITWKRVLDMNDRALRNIVVGLGGKANGVPREDGFDITVASEIMAILCLATDL 212
Query: 287 EDLYNRLSRMMVAEDKEGRPVTLDDLAAKQAGA 319
DL RL R++VA ++G PVT DL AGA
Sbjct: 213 ADLKERLGRIVVAYTRDGEPVTAKDLGV--AGA 243
Score = 99.8 bits (250), Expect = 5e-23
Identities = 30/46 (65%), Positives = 33/46 (71%), Gaps = 1/46 (2%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTFACVRQPSQGPTFGIKG 46
ITPTP GEGK+TTTIGL QAL K A +R+PS GP FGIKG
Sbjct: 62 ITPTPAGEGKTTTTIGLGQAL-NRLGKKAIAALREPSLGPVFGIKG 106
Score = 51.7 bits (125), Expect = 3e-07
Identities = 20/42 (47%), Positives = 29/42 (69%), Gaps = 2/42 (4%)
Query: 313 AAKQAGAHDAVVCENWAKGGAGAADLADAVIKAT-ELKDKQF 353
++AGA +A V E+WAKGG GA +LA+AV++A E + F
Sbjct: 395 LCEEAGA-EAAVSEHWAKGGEGAIELAEAVVEACIEEQPSNF 435
>gnl|CDD|238266 cd00477, FTHFS, Formyltetrahydrofolate synthetase (FTHFS) catalyzes
the ATP-dependent activation of formate ion via its
addition to the N10 position of tetrahydrofolate. FTHFS
is a highly expressed key enzyme in both the
Wood-Ljungdahl pathway of autotrophic CO2 fixation
(acetogenesis) and the glycine synthase/reductase
pathways of purinolysis. The key physiological role of
this enzyme in acetogens is to catalyze the formylation
of tetrahydrofolate, an initial step in the reduction of
carbon dioxide and other one-carbon precursors to
acetate. In purinolytic organisms, the enzymatic
reaction is reversed, liberating formate from
10-formyltetrahydrofolate with concurrent production of
ATP.
Length = 524
Score = 271 bits (695), Expect = 5e-87
Identities = 102/149 (68%), Positives = 115/149 (77%), Gaps = 10/149 (6%)
Query: 55 GLTGAMAVLLKDAVQPNLMQTLEGTPVMVHAGPFANIAHGCSSVVADLIALKLVGAEGYV 114
G+ GAMAVLLKDA++PNL+QTLEGTP VH GPFANIAHGC+S++AD IALKL YV
Sbjct: 223 GVAGAMAVLLKDAIKPNLVQTLEGTPAFVHGGPFANIAHGCNSIIADKIALKL---ADYV 279
Query: 115 VTEAGFGSDIGMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTE 174
VTEAGFG+D+G EKFFNIKCR SG PDAVVLV TVRALKMHGG P V G E
Sbjct: 280 VTEAGFGADLGAEKFFNIKCRYSGLKPDAVVLVATVRALKMHGGVPKVTLGL-------E 332
Query: 175 ENLDLVQKGCVNLEKHVSNGLKFGVPVVV 203
ENL+ ++KG NL KH+ N KFGVPVVV
Sbjct: 333 ENLEALEKGFANLRKHIENIKKFGVPVVV 361
Score = 109 bits (275), Expect = 2e-26
Identities = 47/122 (38%), Positives = 61/122 (50%), Gaps = 29/122 (23%)
Query: 234 EITKFVRLNINPDTISWRRV-------------GQSPTEKNMERSTGFDISVASEVMAAL 280
I RL+I+P I+W+RV G E + R TGFDI+VASE+MA L
Sbjct: 131 HIHHGNRLDIDPRRITWKRVLDVNDRALRKIVIGLGGKENGVPRETGFDITVASEIMAIL 190
Query: 281 ALSKNLEDLYNRLSRMMVAEDKEGRPVTLDDLAAKQAGAHDAVVCENWAKGGAGAADLAD 340
L+ +LEDL RL R++VA K+G PVT +DL GA A L D
Sbjct: 191 CLATDLEDLKERLGRIVVAYSKDGEPVTAEDLGV----------------AGAMAVLLKD 234
Query: 341 AV 342
A+
Sbjct: 235 AI 236
Score = 100 bits (251), Expect = 3e-23
Identities = 35/46 (76%), Positives = 38/46 (82%), Gaps = 1/46 (2%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTFACVRQPSQGPTFGIKG 46
ITPTP GEGK+TTTIGLAQAL AH K AC+R+PS GPTFGIKG
Sbjct: 46 ITPTPAGEGKTTTTIGLAQALNAH-GKKAIACLREPSLGPTFGIKG 90
Score = 49.1 bits (118), Expect = 2e-06
Identities = 20/35 (57%), Positives = 27/35 (77%), Gaps = 1/35 (2%)
Query: 313 AAKQAGAHDAVVCENWAKGGAGAADLADAVIKATE 347
A++AGA AV E+WA+GG GA +LA+AVI+A E
Sbjct: 380 LAEEAGAFVAV-SEHWAEGGKGAVELAEAVIEACE 413
>gnl|CDD|225354 COG2759, MIS1, Formyltetrahydrofolate synthetase [Nucleotide
transport and metabolism].
Length = 554
Score = 254 bits (650), Expect = 5e-80
Identities = 98/149 (65%), Positives = 113/149 (75%), Gaps = 11/149 (7%)
Query: 55 GLTGAMAVLLKDAVQPNLMQTLEGTPVMVHAGPFANIAHGCSSVVADLIALKLVGAEGYV 114
+ GAMA LLKDA++PNL+QTLEGTP VH GPFANIAHGC+S++A ALKL YV
Sbjct: 237 KVEGAMAALLKDAIKPNLVQTLEGTPAFVHGGPFANIAHGCNSIIATKTALKLA---DYV 293
Query: 115 VTEAGFGSDIGMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTE 174
VTEAGFG+D+G EKFF+IKCR+SG PDAVVLV TVRALKMHGG P K + TE
Sbjct: 294 VTEAGFGADLGAEKFFDIKCRSSGLKPDAVVLVATVRALKMHGGVP--------KEDLTE 345
Query: 175 ENLDLVQKGCVNLEKHVSNGLKFGVPVVV 203
EN+D V+KG NL KH+ N KFGVPVVV
Sbjct: 346 ENVDAVKKGFANLLKHIENIKKFGVPVVV 374
Score = 94.3 bits (235), Expect = 3e-21
Identities = 45/120 (37%), Positives = 59/120 (49%), Gaps = 30/120 (25%)
Query: 240 RLNINPDTISWRRV-------------GQSPTEKNMERSTGFDISVASEVMAALALSKNL 286
L I+P I+W+RV G E + R GFDI+VASE+MA L L+ +L
Sbjct: 151 ELGIDPRRITWKRVVDMNDRALRSIVVGLGGPENGVPREDGFDITVASEIMAILCLATDL 210
Query: 287 EDLYNRLSRMMVAEDKEGRPVTLDDLAAKQAGAHDAVVCENWAKGGAGAADLADAVIKAT 346
+DL RL R+++A D +G+PVT DL GA AA L DA IK
Sbjct: 211 KDLKERLGRIVIAYDYDGKPVTAGDLKV----------------EGAMAALLKDA-IKPN 253
Score = 85.8 bits (213), Expect = 2e-18
Identities = 28/46 (60%), Positives = 31/46 (67%), Gaps = 1/46 (2%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTFACVRQPSQGPTFGIKG 46
ITPTP GEGK+TTTIGL AL K +R+PS GP FGIKG
Sbjct: 60 ITPTPAGEGKTTTTIGLVDAL-NKLGKKAIIALREPSLGPVFGIKG 104
Score = 45.0 bits (107), Expect = 4e-05
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 313 AAKQAGAHDAVVCENWAKGGAGAADLADAVIKATELKDKQF 353
++ G + + E WAKGG G +LA V++A E D +F
Sbjct: 393 LCEEHGV-EVALSEVWAKGGEGGIELAKKVVEAIEQNDSEF 432
>gnl|CDD|178359 PLN02759, PLN02759, Formate--tetrahydrofolate ligase.
Length = 637
Score = 252 bits (646), Expect = 1e-78
Identities = 103/149 (69%), Positives = 121/149 (81%)
Query: 55 GLTGAMAVLLKDAVQPNLMQTLEGTPVMVHAGPFANIAHGCSSVVADLIALKLVGAEGYV 114
G+ GA+ VL+KDA+ P LMQTLEGTPV+VHAGPFANIAHG SS+VAD IALKLVG G+V
Sbjct: 307 GVGGALTVLMKDAIHPTLMQTLEGTPVLVHAGPFANIAHGNSSIVADQIALKLVGPGGFV 366
Query: 115 VTEAGFGSDIGMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTE 174
VTEAGFG+DIG EKF NIKCR SG P V+V TVRALKMHGGGP+VV+G+PL YT
Sbjct: 367 VTEAGFGADIGTEKFMNIKCRYSGLKPQCAVIVATVRALKMHGGGPAVVAGKPLDHAYTT 426
Query: 175 ENLDLVQKGCVNLEKHVSNGLKFGVPVVV 203
EN++LV+ GCVNL +H+ N +GV VVV
Sbjct: 427 ENVELVEAGCVNLARHIENTKSYGVNVVV 455
Score = 156 bits (395), Expect = 2e-42
Identities = 63/127 (49%), Positives = 82/127 (64%), Gaps = 13/127 (10%)
Query: 199 VPVVVKGKREFSIIQRRRLLRLDINRTDPNTLTPEEITKFVRLNINPDTISWRRV----- 253
P +GKR F+ + RRL +L I++TDP+ LTPEE KF RL+I+P +I+WRRV
Sbjct: 180 CPANKEGKRSFAAVMFRRLKKLGISKTDPDELTPEERKKFARLDIDPASITWRRVMDVND 239
Query: 254 --------GQSPTEKNMERSTGFDISVASEVMAALALSKNLEDLYNRLSRMMVAEDKEGR 305
GQ P EK M R TGFDI+VASE+MA LAL+ +L D+ RL +M++ K G
Sbjct: 240 RFLRKITVGQGPEEKGMTRETGFDITVASEIMAVLALTTSLADMRERLGKMVIGNSKAGE 299
Query: 306 PVTLDDL 312
PVT DDL
Sbjct: 300 PVTADDL 306
Score = 97.1 bits (242), Expect = 5e-22
Identities = 36/46 (78%), Positives = 38/46 (82%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTFACVRQPSQGPTFGIKG 46
ITPTPLGEGKSTTTIGL QAL A+ K C+RQPSQGPTFGIKG
Sbjct: 77 ITPTPLGEGKSTTTIGLCQALGAYLDKKVVTCLRQPSQGPTFGIKG 122
Score = 52.1 bits (125), Expect = 3e-07
Identities = 21/35 (60%), Positives = 24/35 (68%)
Query: 313 AAKQAGAHDAVVCENWAKGGAGAADLADAVIKATE 347
AA AGA DAV+C + A GG GA DL +AV KA E
Sbjct: 474 AALAAGAFDAVLCTHHAHGGKGAVDLGEAVQKACE 508
>gnl|CDD|237403 PRK13505, PRK13505, formate--tetrahydrofolate ligase; Provisional.
Length = 557
Score = 242 bits (620), Expect = 1e-75
Identities = 93/149 (62%), Positives = 113/149 (75%), Gaps = 11/149 (7%)
Query: 55 GLTGAMAVLLKDAVQPNLMQTLEGTPVMVHAGPFANIAHGCSSVVADLIALKLVGAEGYV 114
+ GAMA+LLKDA++PNL+QTLEGTP VH GPFANIAHGC+SV+A ALKL A+ YV
Sbjct: 240 KVEGAMALLLKDAIKPNLVQTLEGTPAFVHGGPFANIAHGCNSVLATKTALKL--AD-YV 296
Query: 115 VTEAGFGSDIGMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTE 174
VTEAGFG+D+G EKF +IKCR +G PDAVV+V TVRALKMHGG K + E
Sbjct: 297 VTEAGFGADLGAEKFLDIKCRKAGLKPDAVVIVATVRALKMHGGVA--------KDDLKE 348
Query: 175 ENLDLVQKGCVNLEKHVSNGLKFGVPVVV 203
EN++ ++KG NLE+H+ N KFGVPVVV
Sbjct: 349 ENVEALKKGFANLERHIENIRKFGVPVVV 377
Score = 87.2 bits (217), Expect = 7e-19
Identities = 36/92 (39%), Positives = 50/92 (54%), Gaps = 15/92 (16%)
Query: 241 LNINPDTISWRRV-------------GQSPTEKNMERSTGFDISVASEVMAALALSKNLE 287
L I+P I+W+RV G + R GFDI+VASE+MA L L+ +L+
Sbjct: 155 LGIDPRRITWKRVLDMNDRALRNIVVGLGGPANGVPREDGFDITVASEIMAILCLATDLK 214
Query: 288 DLYNRLSRMMVAEDKEGRPVTLDDLAAKQAGA 319
DL RL R++V +G+PVT+ DL GA
Sbjct: 215 DLKERLGRIVVGYTYDGKPVTVKDLKV--EGA 244
Score = 83.7 bits (208), Expect = 1e-17
Identities = 27/46 (58%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTFACVRQPSQGPTFGIKG 46
I PTP GEGKST T+GL AL K T +R+PS GP FGIKG
Sbjct: 63 INPTPAGEGKSTVTVGLGDAL-NKIGKKTVIALREPSLGPVFGIKG 107
Score = 44.0 bits (105), Expect = 9e-05
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 309 LDDLAAKQAGAHDAVVCENWAKGGAGAADLADAVIKATELKDKQF 353
L +L + G + E WAKGG G +LA+ V++ E + F
Sbjct: 393 LKELCEEL-GVE-VALSEVWAKGGEGGVELAEKVVELIEEGESNF 435
>gnl|CDD|240394 PTZ00386, PTZ00386, formyl tetrahydrofolate synthetase;
Provisional.
Length = 625
Score = 241 bits (617), Expect = 2e-74
Identities = 100/149 (67%), Positives = 116/149 (77%), Gaps = 8/149 (5%)
Query: 55 GLTGAMAVLLKDAVQPNLMQTLEGTPVMVHAGPFANIAHGCSSVVADLIALKLVGAEGYV 114
G GAM VL+KD ++P LMQTLEGTPV+VHAGPF NIAHG SS+VAD IALKL G +G+V
Sbjct: 302 GCAGAMTVLMKDTIEPTLMQTLEGTPVLVHAGPFGNIAHGNSSIVADQIALKLAGQDGFV 361
Query: 115 VTEAGFGSDIGMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTE 174
+TEAGFG+DIG EKFFNIKCRTSG PDA VLV TVRALK HGG VV+G+
Sbjct: 362 LTEAGFGADIGCEKFFNIKCRTSGLKPDAAVLVATVRALKFHGGVEPVVAGK-------- 413
Query: 175 ENLDLVQKGCVNLEKHVSNGLKFGVPVVV 203
ENL+ V+KG NL++H+ N KFGVPVVV
Sbjct: 414 ENLEAVRKGLSNLQRHIQNIRKFGVPVVV 442
Score = 143 bits (362), Expect = 5e-38
Identities = 63/128 (49%), Positives = 81/128 (63%), Gaps = 15/128 (11%)
Query: 205 GKREFSIIQRRRLLRLDINRTDPNTLTPEEITKFVRLNINPDTISWRRV----------- 253
++F+ I +RL +L I++TDP LT EE +F RL+I+PDTISWRRV
Sbjct: 181 ELKKFTPIMLKRLEKLGISKTDPKQLTEEERVRFARLDIDPDTISWRRVTDVNDRMLREI 240
Query: 254 --GQSPTEKNMERSTGFDISVASEVMAALALSKNLEDLYNRLSRMMVAEDKEGRPVTLDD 311
GQ EK + R TGFDISVASEVMA LAL+ +L D+ RL ++VA+ K G PVT +D
Sbjct: 241 TIGQGKEEKGITRKTGFDISVASEVMAILALATDLADMRQRLGAIVVAKSKSGEPVTAED 300
Query: 312 LAAKQAGA 319
L AGA
Sbjct: 301 LGC--AGA 306
Score = 97.6 bits (243), Expect = 3e-22
Identities = 38/46 (82%), Positives = 42/46 (91%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTFACVRQPSQGPTFGIKG 46
+ PTPLGEGKSTTTIGLAQ+L AH H+ TFAC+RQPSQGPTFGIKG
Sbjct: 76 MNPTPLGEGKSTTTIGLAQSLGAHLHRKTFACIRQPSQGPTFGIKG 121
Score = 52.5 bits (126), Expect = 2e-07
Identities = 23/50 (46%), Positives = 33/50 (66%)
Query: 298 VAEDKEGRPVTLDDLAAKQAGAHDAVVCENWAKGGAGAADLADAVIKATE 347
+ D + + +LA ++ GA D VV ++WAKGGAGA DLA A+I+ TE
Sbjct: 447 FSTDTDAELELVKELALQEGGAADVVVTDHWAKGGAGAVDLAQALIRVTE 496
>gnl|CDD|184098 PRK13507, PRK13507, formate--tetrahydrofolate ligase; Provisional.
Length = 587
Score = 218 bits (558), Expect = 4e-66
Identities = 87/146 (59%), Positives = 106/146 (72%), Gaps = 3/146 (2%)
Query: 58 GAMAVLLKDAVQPNLMQTLEGTPVMVHAGPFANIAHGCSSVVADLIALKLVGAEGYVVTE 117
GAM + A+ PNL+QT+EG PV VHAGPFANIA G SS++AD + LKL Y VTE
Sbjct: 264 GAMTAWMVRAINPNLLQTIEGQPVFVHAGPFANIAIGQSSIIADRVGLKL---ADYHVTE 320
Query: 118 AGFGSDIGMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTEENL 177
+GFG+DIG EKF+N+KCR SG PD V+V T+RALKMHGGGP VV G+PL EYT+EN+
Sbjct: 321 SGFGADIGFEKFWNLKCRLSGLKPDCAVIVATIRALKMHGGGPKVVPGKPLPEEYTKENV 380
Query: 178 DLVQKGCVNLEKHVSNGLKFGVPVVV 203
LV+KGC NL H+ K G+ VV
Sbjct: 381 GLVEKGCANLLHHIGTVKKSGINPVV 406
Score = 76.7 bits (189), Expect = 3e-15
Identities = 30/47 (63%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTFACVRQPSQGPTFGIKGS 47
ITPTPLGEGKSTTT+GL Q L + K +RQPS GPT IKGS
Sbjct: 71 ITPTPLGEGKSTTTMGLVQGLGK-RGKKVSGAIRQPSGGPTMNIKGS 116
Score = 64.7 bits (158), Expect = 2e-11
Identities = 24/47 (51%), Positives = 37/47 (78%)
Query: 266 TGFDISVASEVMAALALSKNLEDLYNRLSRMMVAEDKEGRPVTLDDL 312
+GF I+V+SEVMA L+++ +L+DL R+ +++VA DK G+PVT DL
Sbjct: 214 SGFGIAVSSEVMAILSVATDLKDLRERIGKIVVAYDKNGKPVTTADL 260
Score = 42.8 bits (101), Expect = 2e-04
Identities = 20/35 (57%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 313 AAKQAGAHDAVVCENWAKGGAGAADLADAVIKATE 347
A+QAGA AV +W KGG GA +LADAVI A
Sbjct: 425 LAEQAGARVAV-SRHWEKGGEGALELADAVIDACN 458
>gnl|CDD|237404 PRK13506, PRK13506, formate--tetrahydrofolate ligase; Provisional.
Length = 578
Score = 212 bits (543), Expect = 4e-64
Identities = 82/149 (55%), Positives = 104/149 (69%), Gaps = 3/149 (2%)
Query: 55 GLTGAMAVLLKDAVQPNLMQTLEGTPVMVHAGPFANIAHGCSSVVADLIALKLVGAEGYV 114
G+ GAM V++KDA++P LMQTLEG P ++HAGPFANIAHG SS++AD IALKL YV
Sbjct: 253 GVAGAMTVIMKDAIEPTLMQTLEGVPCLIHAGPFANIAHGNSSIIADRIALKLAD---YV 309
Query: 115 VTEAGFGSDIGMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTE 174
VTE GFGSD+G EKF NIK R SGK PD VLV T+RALK + G + GQ L
Sbjct: 310 VTEGGFGSDMGFEKFCNIKARQSGKAPDCAVLVATLRALKANSGLYDLRPGQALPDSINA 369
Query: 175 ENLDLVQKGCVNLEKHVSNGLKFGVPVVV 203
+ ++ G NL+ H++N ++G+PVVV
Sbjct: 370 PDQARLEAGFANLKWHINNVAQYGLPVVV 398
Score = 81.6 bits (202), Expect = 5e-17
Identities = 36/100 (36%), Positives = 58/100 (58%), Gaps = 15/100 (15%)
Query: 240 RLNINPDTISWRRV-------------GQSPTEKNMERSTGFDISVASEVMAALALSKNL 286
L+I+P+ I W+RV G ER GFDI+ ASE+MA LALS++L
Sbjct: 167 ALDIDPEQILWKRVVDHNDRALRMITVGLGENGNGPEREDGFDITAASELMAILALSRDL 226
Query: 287 EDLYNRLSRMMVAEDKEGRPVTLDDLAAKQAGAHDAVVCE 326
+D+ R+ R+++A + +G+P+T +DL AGA ++ +
Sbjct: 227 KDMRQRIGRLVLAYNLQGQPITAEDLGV--AGAMTVIMKD 264
Score = 80.8 bits (200), Expect = 1e-16
Identities = 31/46 (67%), Positives = 34/46 (73%), Gaps = 1/46 (2%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTFACVRQPSQGPTFGIKG 46
ITPTPLGEGK+ TTIGL Q L A K AC+RQPS GP FG+KG
Sbjct: 62 ITPTPLGEGKTVTTIGLTQGLNALGQK-VCACIRQPSMGPVFGVKG 106
Score = 39.2 bits (92), Expect = 0.003
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 313 AAKQAGAHDAVVCENWAKGGAGAADLADAVIKATE 347
A GA + E +A+GG GA LA AV++A E
Sbjct: 417 AVLLTGAFGCEISEAFAQGGEGATALAQAVVRACE 451
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
of proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 34.3 bits (79), Expect = 0.014
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 7 GEGKSTTTIGLAQALAAHKHK 27
G GK+T LA ALA +
Sbjct: 9 GVGKTTLAANLAAALAKRGKR 29
Score = 28.9 bits (65), Expect = 1.1
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 113 YVVTEAGFGSDIGMEKFFNIKCRTSGKIPDAVVLVTTVRALKMHGG 158
YV+ + G + + C + D V++VTT AL + G
Sbjct: 36 YVLIDTPPGLGLLVLL-----CLLALLAADLVIIVTTPEALAVLGA 76
>gnl|CDD|238997 cd02042, ParA, ParA and ParB of Caulobacter crescentus belong to
a conserved family of bacterial proteins implicated in
chromosome segregation. ParB binds to DNA sequences
adjacent to the origin of replication and localizes to
opposite cell poles shortly following the initiation of
DNA replication. ParB regulates the ParA ATPase
activity by promoting nucleotide exchange in a fashion
reminiscent of the exchange factors of eukaryotic G
proteins. ADP-bound ParA binds single-stranded DNA,
whereas the ATP-bound form dissociates ParB from its
DNA binding sites. Increasing the fraction of ParA-ADP
in the cell inhibits cell division, suggesting that
this simple nucleotide switch may regulate cytokinesis.
ParA shares sequence similarity to a conserved and
widespread family of ATPases which includes the repA
protein of the repABC operon in R. etli Sym plasmid.
This operon is involved in the plasmid replication and
partition.
Length = 104
Score = 34.1 bits (79), Expect = 0.023
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 7 GEGKSTTTIGLAQALAAHKHK 27
G GK+TT + LA ALA +
Sbjct: 10 GVGKTTTAVNLAAALARRGKR 30
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 34.7 bits (80), Expect = 0.045
Identities = 22/73 (30%), Positives = 30/73 (41%), Gaps = 13/73 (17%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTF---ACVRQPSQGPTFGIKGSHMALLLSGLT 57
+T G GKST + LA ALA K A +R PS G+ L
Sbjct: 62 VTSGKGGVGKSTVAVNLAAALAQ-LGKRVLLLDADLRGPSIPRMLGL---------ENLP 111
Query: 58 GAMAVLLKDAVQP 70
G +L +A++P
Sbjct: 112 GLTELLAGEALEP 124
>gnl|CDD|216631 pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain.
This family consists of various cobyrinic acid
a,c-diamide synthases. These include CbiA and CbiP from
S.typhimurium, and CobQ from R. capsulatus. These
amidases catalyze amidations to various side chains of
hydrogenobyrinic acid or cobyrinic acid a,c-diamide in
the biosynthesis of cobalamin (vitamin B12) from
uroporphyrinogen III. Vitamin B12 is an important
cofactor and an essential nutrient for many plants and
animals and is primarily produced by bacteria. The
family also contains dethiobiotin synthetases as well
as the plasmid partitioning proteins of the MinD/ParA
family.
Length = 217
Score = 33.2 bits (76), Expect = 0.15
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 7 GEGKSTTTIGLAQALAAHKHK 27
G GK+T LA+ALA ++
Sbjct: 9 GVGKTTLAANLARALAKRGYR 29
>gnl|CDD|224113 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 31.7 bits (72), Expect = 0.40
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 7 GEGKSTTTIGLAQALAAHKHKNT 29
G GK+TT + LA ALA K
Sbjct: 13 GVGKTTTAVNLAAALAKRGGKKV 35
>gnl|CDD|132063 TIGR03018, pepcterm_TyrKin, exopolysaccharide/PEP-CTERM locus
tyrosine autokinase. Members of this protein family
are related to a known protein-tyrosine autokinase and
to numerous homologs from exopolysaccharide
biosynthesis region proteins, many of which are
designated as chain length determinants. Most members
of this family contain a short region, immediately
C-terminal to the region modeled here, with an
abundance of Tyr residues. These C-terminal tyrosine
residues are likely to be autophosphorylation sites.
Some members of this family are fusion proteins.
Length = 207
Score = 31.1 bits (71), Expect = 0.66
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTF---ACVRQPSQGPTFGIKGS 47
+T + GEGKS T I LA +LA K A +R+PS T G++
Sbjct: 40 VTSSLPGEGKSFTAINLAISLAQEYDKTVLLIDADLRRPSLHRTLGLEAE 89
>gnl|CDD|236171 PRK08168, PRK08168, NADH dehydrogenase subunit L; Provisional.
Length = 516
Score = 31.2 bits (71), Expect = 0.80
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 12/79 (15%)
Query: 15 IGLAQALAAHKHKN-TFACVRQPSQGPTFGIKGSHMALLLSGLTGAMAVLLKDAVQPN-- 71
+ A ALA + + + + + +G+ +L + L +AV+LK A P
Sbjct: 167 LLAAAALAYLEVGSLSLSALWA-----HLAAQGASPSLQAAALLLVLAVILKTAQLPVHG 221
Query: 72 -LMQTLEG-TPV--MVHAG 86
L+Q +E TPV ++HAG
Sbjct: 222 WLIQVMEAPTPVSALLHAG 240
>gnl|CDD|220262 pfam09485, CRISPR_Cse2, CRISPR-associated protein Cse2
(CRISPR_cse2). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This family of proteins,
represented by CT1973 from Chlorobaculum tepidum, is
encoded by genes found in the CRISPR/Cas subtype Ecoli
regions of many bacteria (most of which are mesophiles),
and not in Archaea. It is designated Cse2.
Length = 143
Score = 30.0 bits (68), Expect = 0.82
Identities = 18/65 (27%), Positives = 25/65 (38%), Gaps = 3/65 (4%)
Query: 269 DISVASEV-MAALALSKNLEDLYNRLSRMMVAEDKEGRPVTLDDLAA--KQAGAHDAVVC 325
D S SE L + ++L RL R++ +G PV DLA V
Sbjct: 76 DKSDVSERRFRQLLRADTPDELLRRLRRLVRLLRGDGVPVDYADLARDLLYWNDETQRVR 135
Query: 326 ENWAK 330
WA+
Sbjct: 136 RRWAR 140
>gnl|CDD|240009 cd04638, CBS_pair_25, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 106
Score = 28.9 bits (65), Expect = 1.3
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 16/74 (21%)
Query: 188 EKHVSNGLKFGVPVVVKGKREFSIIQRRRLLR-------LDINRTDPNTLTPEE-ITKFV 239
E VS GVPVV K II R+ LLR + DP T++P++ + +
Sbjct: 21 EYKVS-----GVPVVKKSGELVGIITRKDLLRNPEEEQLALLMTRDPPTVSPDDDVKEAA 75
Query: 240 RLNINPDTISWRRV 253
+L + + RRV
Sbjct: 76 KLMVENNI---RRV 86
>gnl|CDD|238994 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is
a homologue of the Fer4_NifH superfamily. Like the
other members of the superfamily, MRP contains a
ATP-binding domain at the N-termini. It is found in
bacteria as a membrane-spanning protein and functions
as a Na+/H+ antiporter.
Length = 169
Score = 29.4 bits (67), Expect = 1.9
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 7 GEGKSTTTIGLAQALAAHKHK 27
G GKST + LA ALA +K
Sbjct: 10 GVGKSTVAVNLALALAKLGYK 30
>gnl|CDD|130758 TIGR01697, PNPH-PUNA-XAPA, inosine/guanosine/xanthosine
phosphorylase family. This model is a subset of the
subfamily represented by pfam00896 (phosphorylase family
2). This model excludes the methylthioadenosine
phosphorylases (MTAP, TIGR01684) which are believed
toplay a specific role in the recycling of methionine
from methylthioadenosine. In this subfamily is found
three clades of purine phosphorylases based on a
neighbor-joining tree using the MTAP family as an
outgroup. The highest-branching clade (TIGR01698)
consists of a group of sequences from both gram positive
and gram negative bacteria which have been annotated as
purine nucleotide phosphorylases but have not been
further characterized as to substrate specificity. Of
the two remaining clades, one is xanthosine
phosphorylase (XAPA, TIGR01699), is limited to certain
gamma proteobacteria and constitutes a special purine
phosphorylase found in a specialized operon for
xanthosine catabolism. The enzyme also acts on the same
purines (inosine and guanosine) as the other
characterized members of this subfamily, but is only
induced when xanthosine must be degraded. The remaining
and largest clade consists of purine nucleotide
phosphorylases (PNPH, TIGR01700) from metazoa and
bacteria which act primarily on guanosine and inosine
(and do not act on adenosine). Sequences from
Clostridium (GP:15025051) and Thermotoga (OMNI:TM1596)
fall between these last two clades and are
uncharacterized with respect to substrate range and
operon.
Length = 248
Score = 29.2 bits (66), Expect = 2.6
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 75 TLEGTPVMVHAGPFANIAHGCSSVVADLI-ALKLVGAEGYVVTEA 118
L G PV+ G F + V + +KL+G E VVT A
Sbjct: 47 RLGGKPVVCMQGRFHYYEGYDMATVTFPVRVMKLLGVEILVVTNA 91
>gnl|CDD|130080 TIGR01007, eps_fam, capsular exopolysaccharide family. This
model describes the capsular exopolysaccharide proteins
in bacteria. The exopolysaccharide gene cluster
consists of several genes which encode a number of
proteins which regulate the exoploysaccharide
biosynthesis(EPS). Atleast 13 genes espA to espM in
streptococcus species seem to direct the EPS proteins
and all of which share high homology. Functional roles
were characterized by gene disruption experiments which
resulted in exopolysaccharide-deficient phenotypes
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 204
Score = 28.9 bits (65), Expect = 3.3
Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 5/77 (6%)
Query: 1 ITPTPLGEGKSTTTIGLAQALAAHKHKNTF--ACVRQPSQGPTFGIKGSHMAL--LLSGL 56
IT GEGKSTT+ +A A A +K +R TF + L LSG
Sbjct: 22 ITSVKPGEGKSTTSANIAVAFAQAGYKTLLIDGDMRNSVMSGTFKSQNKITGLTNFLSG- 80
Query: 57 TGAMAVLLKDAVQPNLM 73
T ++ + D NL
Sbjct: 81 TTDLSDAICDTNIENLF 97
>gnl|CDD|226848 COG4424, COG4424, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 250
Score = 29.1 bits (65), Expect = 3.4
Identities = 24/83 (28%), Positives = 32/83 (38%), Gaps = 8/83 (9%)
Query: 141 PDAVVLVTTVRALKMHGGGPSVVSGQPLKPEYTEENLDLVQKGCVNLEKHVSNGLK---- 196
P+A V A G P+ V G L L+Q+ V L S+GL+
Sbjct: 59 PEAATPVAWFEAAITKGSTPNGVFGLKLMRNQDA----LLQQLAVQLPDRSSDGLRIEDA 114
Query: 197 FGVPVVVKGKREFSIIQRRRLLR 219
FG P+ V R + Q L R
Sbjct: 115 FGEPLFVHLHRPDKVSQAVSLWR 137
>gnl|CDD|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor. Members of
this protein family are the RNA polymerase sigma factor
F. Sigma-F is specifically and universally a component
of the Firmicutes lineage endospore formation program,
and is expressed in the forespore to turn on expression
of dozens of genes. It is closely homologous to sigma-G,
which is also expressed in the forespore [Transcription,
Transcription factors, Cellular processes, Sporulation
and germination].
Length = 231
Score = 28.5 bits (64), Expect = 4.2
Identities = 35/153 (22%), Positives = 64/153 (41%), Gaps = 38/153 (24%)
Query: 178 DLVQKGCVNLEKHVSN-----GLKF---GVPVVVKGKREFSIIQRRRLLRLD----INRT 225
DL Q GC+ L K + +KF VP+++ + +R LR D ++R+
Sbjct: 40 DLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMG--------EIKRFLRDDGIIKVSRS 91
Query: 226 DPNTLTPEEITKFVRLNINPDTISWRRVGQSPTEKNMERSTGFDISVASEVMAALALSKN 285
E K + +S + +G+ PT + + G E++ AL +++
Sbjct: 92 -----LKELARKIRY---MKEELS-KELGREPTINELAEALGVSP---EEIVMALESARS 139
Query: 286 LEDLYNRLSRMMVAEDKEGRPVTLDDLAAKQAG 318
+ LY+ V +D +G P+ L D A +
Sbjct: 140 PQSLYD-----TVHQD-DGDPIYLLDQIADKGS 166
>gnl|CDD|234078 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G
subfamily. This group of similar sigma-70 factors
includes clades found in Bacilli (including the
sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as
well as SigB:TIGR02941), and the high GC gram positive
bacteria (Actinobacteria) where a variable number of
them are found depending on the lineage.
Length = 227
Score = 28.7 bits (65), Expect = 4.3
Identities = 46/164 (28%), Positives = 65/164 (39%), Gaps = 45/164 (27%)
Query: 178 DLVQKGCVNLEKHVSN-----GLKF---GVPVVVKG--KREF-----SIIQRRRL--LRL 220
DLVQ G + L K + G+KF VP ++ G KR F ++ RRL L +
Sbjct: 32 DLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIM-GEIKRFFRDDTWAVRVPRRLKELGV 90
Query: 221 DINRTDPNTLTPEEITKFVRLNINPDTISWRRVGQSPTEKNMERSTGFDISVASEVMAAL 280
IN+ EE+T+ R+G+SPT + G EV+ AL
Sbjct: 91 KINKAT------EELTQ--------------RLGRSPTIAEIAERLGVSE---EEVVEAL 127
Query: 281 ALSKNLEDLYNRLSRMMVAEDKEGRPVTLDDLAAKQAGAHDAVV 324
Y LS ED +G P+ L D + A + V
Sbjct: 128 EAGNA----YQALSLDASIEDDDGDPIALLDTLGDEDDALETVE 167
>gnl|CDD|131324 TIGR02271, TIGR02271, conserved domain. This model describes an
uncharacterized domain, sometimes found in association
with a PRC-barrel domain (pfam05239, which is also found
in rRNA processing protein RimM and in a photosynthetic
reaction center complex protein). This domain is found
in proteins from Bacillus subtilis, Deinococcus
radiodurans, Nostoc sp. PCC 7120, Myxococcus xanthus,
and several other species. The function is not known.
Length = 115
Score = 27.5 bits (61), Expect = 5.5
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 167 PLKPEYTEENLDLVQKGCVNLEKHVSNGLK-FGVPVVVKGKREFSIIQRRRLLRLDINRT 225
L+ E + N + VQ G V L K VS+ K +PV + E +I+RR + N
Sbjct: 2 KLRKEQLDVNKEWVQTGEVELGKEVSSEQKTVDIPV----EHEEVVIERR---PVTDNEA 54
Query: 226 DPNTLTPEEITK 237
+ + +E+ +
Sbjct: 55 SDDPIGDKEVIR 66
>gnl|CDD|233683 TIGR02005, PTS-IIBC-alpha, PTS system, alpha-glucoside-specific
IIBC component. This model represents a family of fused
PTS enzyme II B and C domains. A gene from Clostridium
has been partially characterized as a maltose
transporter, while genes from Fusobacterium and
Klebsiella have been proposed to transport the five
non-standard isomers of sucrose [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 524
Score = 28.6 bits (64), Expect = 6.2
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 269 DISVASEVMAALALSKNLEDLYNRLSRMMVAEDKEGRPVTLDDLAAKQAGAHDAV 323
A+ + AL +N++D+ N +R+ ++ E + LDD K+AGAH V
Sbjct: 447 GNDKAAYFLQALGGKENIKDVTNCATRLRISVKDESK--VLDDEVFKKAGAHGVV 499
>gnl|CDD|236732 PRK10662, PRK10662, beta-lactam binding protein AmpH; Provisional.
Length = 378
Score = 28.1 bits (63), Expect = 6.8
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 273 ASEVMAALALSKNLEDLYNRLSR-----MMVAEDKEGRPVTLDDLAAKQAG 318
SEV+ LA ++ L + LS+ V G+P+TL +LA +
Sbjct: 93 TSEVLVKLADDGTVK-LTDPLSKYAPPGARV-PTYNGQPITLLNLATHTSA 141
>gnl|CDD|219756 pfam08237, PE-PPE, PE-PPE domain. This domain is found C terminal
to the PE (pfam00934) and PPE (pfam00823) domains. The
secondary structure of this domain is predicted to be a
mixture of alpha helices and beta strands.
Length = 227
Score = 28.1 bits (63), Expect = 6.9
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 4/77 (5%)
Query: 180 VQKGCVNLEKHVSNGLKFGVPVVVKGKREFSIIQRRRLLRLDINRTDPNTLTPEEITKFV 239
V +G NL + + L G PVVV G + +++ RL DP P++++ FV
Sbjct: 28 VAEGVDNLNAAIRSQLAAGEPVVVFGYSQGALVAALEKARL-AALGDPTAPPPDDLS-FV 85
Query: 240 RLN--INPDTISWRRVG 254
+ P+ R
Sbjct: 86 LIGNPNRPNGGLLARFP 102
>gnl|CDD|150114 pfam09338, Gly_reductase, Glycine/sarcosine/betaine reductase
component B subunits. This is a family of glycine
reductase, sarcosine reductase and betaine reductases.
These enzymes catalyze the following reactions.
sarcosine reductase: Acetyl phosphate + methylamine +
thioredoxin disulphide = N-methylglycine + phosphate +
thioredoxin Acetyl phosphate + NH(3) + thioredoxin
disulphide = glycine + phosphate + thioredoxin. betaine
reductase: Acetyl phosphate + trimethylamine +
thioredoxin disulphide = N,N,N-trimethylglycine +
phosphate + thioredoxin.
Length = 428
Score = 28.1 bits (63), Expect = 7.5
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 95 CSSVVADLIALKLVGAEGYVVTEAGFG 121
SS VA L +++GA+G +V+E GFG
Sbjct: 291 SSSYVAKLA--EMLGADGVIVSEEGFG 315
>gnl|CDD|178267 PLN02661, PLN02661, Putative thiazole synthesis.
Length = 357
Score = 27.9 bits (62), Expect = 8.1
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 6/44 (13%)
Query: 36 PSQGPTFGI------KGSHMALLLSGLTGAMAVLLKDAVQPNLM 73
P GPTFG K +H+AL GL A+ K + P L+
Sbjct: 303 PRMGPTFGAMMISGQKAAHLALKALGLPNALDGTYKPNLHPELV 346
>gnl|CDD|224710 COG1797, CobB, Cobyrinic acid a,c-diamide synthase [Coenzyme
metabolism].
Length = 451
Score = 28.0 bits (63), Expect = 9.4
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 7 GEGKSTTTIGLAQALAAHKHK 27
G GK+T T+GL +AL K
Sbjct: 11 GSGKTTVTLGLMRALRRRGLK 31
>gnl|CDD|185750 cd09237, V_ScBro1_like, Protein-interacting V-domain of
Saccharomyces cerevisiae Bro1 and related domains. This
family contains the V-shaped (V) domain of Saccharomyces
cerevisiae Bro1, and related domains. It belongs to the
V_Alix_like superfamily which also includes the V-domain
of Saccharomyces cerevisiae Rim20 (also known as PalA),
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), and related
domains. Bro1 interacts with the ESCRT (Endosomal
Sorting Complexes Required for Transport) system, and
participates in endosomal trafficking. The mammalian
Alix V-domain (belonging to a different family) contains
a binding site, partially conserved in the superfamily,
for the retroviral late assembly (L) domain YPXnL motif.
The Alix V-domain is also a dimerization domain. Bro1
also has an N-terminal Bro1-like domain, which binds
Snf7, a component of the ESCRT-III complex, and a
C-terminal proline-rich region (PRR). The C-terminal
portion (V-domain and PRR) of S. cerevisiae Bro1
interacts with Doa4, a ubiquitin thiolesterase needed to
remove ubiquitin from MVB cargoes. It interacts with a
YPxL motif in the Doa4s catalytic domain to stimulate
its deubiquitination activity.
Length = 356
Score = 27.6 bits (62), Expect = 9.9
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 5/44 (11%)
Query: 269 DISVASEVMAALALSKNLEDLYNRLSRMMVAEDKEGRPVTLDDL 312
D+ + L K LE+L L+ + KE R L DL
Sbjct: 186 DLDDSQNEQTVLKQIKQLEELLEDLNLI-----KEERQRVLKDL 224
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
0.317 0.133 0.383
Gapped
Lambda K H
0.267 0.0799 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,146,497
Number of extensions: 1793622
Number of successful extensions: 2058
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2032
Number of HSP's successfully gapped: 84
Length of query: 353
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 255
Effective length of database: 6,590,910
Effective search space: 1680682050
Effective search space used: 1680682050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.4 bits)