RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14485
(348 letters)
>gnl|CDD|232973 TIGR00433, bioB, biotin synthase. Catalyzes the last step of the
biotin biosynthesis pathway. All members of the seed
alignment are in the immediate gene neighborhood of a
bioA gene [Biosynthesis of cofactors, prosthetic groups,
and carriers, Biotin].
Length = 296
Score = 450 bits (1160), Expect = e-160
Identities = 144/297 (48%), Positives = 196/297 (65%), Gaps = 5/297 (1%)
Query: 36 NLFNLPFNDLLFRAQKVHRKYFDANEIELAVLLSIKTGGCTEDCGYCPQSTHYNTEITAT 95
L + P DLL AQ++ R +F N+++L +++ K+GGC EDC YC QS HY T I
Sbjct: 2 ELPDEPLLDLLAAAQRIRRHFF-GNKVDLCSIINAKSGGCPEDCKYCAQSAHYKTGIEKY 60
Query: 96 KILSIESVITAAQKAKSDGATRFCMGAAWRELKDRDLDNIENMICEVKK-IGLETCLTLG 154
+LS+E V+ AA+KAK+ GA+RFCM + R DR+ + + I E+K+ GLE C +LG
Sbjct: 61 PLLSVEEVLEAAKKAKAAGASRFCMVTSGRGPSDREFEKVLEAIREIKEETGLEVCASLG 120
Query: 155 MLNENQAYRLKKVGLDYYNHNLDTSPKLYGDIISTRDYENRLNTLKNVRNVGINICCGGI 214
+L+E QA RLK G+D YNHNL+TSP Y +I +T Y++RL TLK R G+++C GGI
Sbjct: 121 LLSEEQAQRLKDAGVDRYNHNLETSPSYYPNICTTHTYDDRLETLKRARKAGLSVCSGGI 180
Query: 215 IGLSESRDQRAELIFQLANLNPYPESVPINNLVQIKGTPLYGSSILDPLEFIRTIAVARI 274
IG+ E+ + R EL F LA L+ +SVPIN LV I GTPL + LDP E +RTIA+ R
Sbjct: 181 IGMGETMEDRIELAFALAELD--VDSVPINFLVPIPGTPLEDAPPLDPEECLRTIALFRF 238
Query: 275 TMPTSRIRMSAGRKEMGETTQAFCFLAGANSIFYGDKLLTTDNTKTNDDSKLLKKLG 331
MP + IR++ GR+ M QA CFLAGANSIF GD LTT + +D ++L+ LG
Sbjct: 239 IMPDAEIRLAGGRELMLRELQALCFLAGANSIFTGD-YLTTAGREAEEDLEMLEDLG 294
>gnl|CDD|185063 PRK15108, PRK15108, biotin synthase; Provisional.
Length = 345
Score = 444 bits (1143), Expect = e-157
Identities = 178/319 (55%), Positives = 238/319 (74%)
Query: 29 WKLDEVINLFNLPFNDLLFRAQKVHRKYFDANEIELAVLLSIKTGGCTEDCGYCPQSTHY 88
W L +V LF P +LLF AQ+VHR++FD +++++ LLSIKTG C EDC YCPQS+ Y
Sbjct: 7 WTLSQVTELFEKPLLELLFEAQQVHRQHFDPRQVQVSTLLSIKTGACPEDCKYCPQSSRY 66
Query: 89 NTEITATKILSIESVITAAQKAKSDGATRFCMGAAWRELKDRDLDNIENMICEVKKIGLE 148
T + A +++ +E V+ +A+KAK+ G+TRFCMGAAW+ +RD+ +E M+ VK +GLE
Sbjct: 67 KTGLEAERLMEVEQVLESARKAKAAGSTRFCMGAAWKNPHERDMPYLEQMVQGVKAMGLE 126
Query: 149 TCLTLGMLNENQAYRLKKVGLDYYNHNLDTSPKLYGDIISTRDYENRLNTLKNVRNVGIN 208
TC+TLG L+E+QA RL GLDYYNHNLDTSP+ YG+II+TR Y+ RL+TL+ VR+ GI
Sbjct: 127 TCMTLGTLSESQAQRLANAGLDYYNHNLDTSPEFYGNIITTRTYQERLDTLEKVRDAGIK 186
Query: 209 ICCGGIIGLSESRDQRAELIFQLANLNPYPESVPINNLVQIKGTPLYGSSILDPLEFIRT 268
+C GGI+GL E+ RA L+ QLANL PESVPIN LV++KGTPL + +D +FIRT
Sbjct: 187 VCSGGIVGLGETVKDRAGLLLQLANLPTPPESVPINMLVKVKGTPLADNDDVDAFDFIRT 246
Query: 269 IAVARITMPTSRIRMSAGRKEMGETTQAFCFLAGANSIFYGDKLLTTDNTKTNDDSKLLK 328
IAVARI MPTS +R+SAGR++M E TQA CF+AGANSIFYG KLLTT N + + D +L +
Sbjct: 247 IAVARIMMPTSYVRLSAGREQMNEQTQAMCFMAGANSIFYGCKLLTTPNPEEDKDLQLFR 306
Query: 329 KLGINTRNIKIKMKNNIKQ 347
KLG+N + + +N +Q
Sbjct: 307 KLGLNPQQTAVLAGDNEQQ 325
>gnl|CDD|215219 PLN02389, PLN02389, biotin synthase.
Length = 379
Score = 405 bits (1043), Expect = e-141
Identities = 158/330 (47%), Positives = 215/330 (65%), Gaps = 2/330 (0%)
Query: 8 SSKESNSIKKNNAISSSQSLIWKLDEVINLFNLPFNDLLFRAQKVHRKYFDANEIELAVL 67
SS + +I AI W DE+ +++ P DLLF +VHR D E++ L
Sbjct: 26 SSSSAAAIAAERAIREGPRNDWTRDEIKEVYDSPLLDLLFHGAQVHRHAHDPREVQQCTL 85
Query: 68 LSIKTGGCTEDCGYCPQSTHYNTEITATKILSIESVITAAQKAKSDGATRFCMGAAWREL 127
LSIKTGGC+EDC YCPQS+ Y+T + A K++S + V+ AA++AK G+TRFCMGAAWR+
Sbjct: 86 LSIKTGGCSEDCSYCPQSSRYDTGVKAQKLMSKDDVLEAAKRAKEAGSTRFCMGAAWRDT 145
Query: 128 --KDRDLDNIENMICEVKKIGLETCLTLGMLNENQAYRLKKVGLDYYNHNLDTSPKLYGD 185
+ + + I + E++ +G+E C TLGML + QA +LK+ GL YNHNLDTS + Y +
Sbjct: 146 VGRKTNFNQILEYVKEIRGMGMEVCCTLGMLEKEQAAQLKEAGLTAYNHNLDTSREYYPN 205
Query: 186 IISTRDYENRLNTLKNVRNVGINICCGGIIGLSESRDQRAELIFQLANLNPYPESVPINN 245
+I+TR Y++RL TL+ VR GI++C GGIIGL E+ + R L+ LA L +PESVPIN
Sbjct: 206 VITTRSYDDRLETLEAVREAGISVCSGGIIGLGEAEEDRVGLLHTLATLPEHPESVPINA 265
Query: 246 LVQIKGTPLYGSSILDPLEFIRTIAVARITMPTSRIRMSAGRKEMGETTQAFCFLAGANS 305
LV +KGTPL ++ E +R IA ARI MP + +R+SAGR QA CFLAGANS
Sbjct: 266 LVAVKGTPLEDQKPVEIWEMVRMIATARIVMPKAMVRLSAGRVRFSMAEQALCFLAGANS 325
Query: 306 IFYGDKLLTTDNTKTNDDSKLLKKLGINTR 335
IF GDKLLTT N + D + K+LG+ +
Sbjct: 326 IFTGDKLLTTPNNDFDADQAMFKELGLIPK 355
>gnl|CDD|223576 COG0502, BioB, Biotin synthase and related enzymes [Coenzyme
metabolism].
Length = 335
Score = 397 bits (1021), Expect = e-139
Identities = 169/306 (55%), Positives = 214/306 (69%), Gaps = 4/306 (1%)
Query: 29 WKLDEVINLFNLPFND-LLFRAQKVHRKYFDANEIELAVLLSIKTGGCTEDCGYCPQSTH 87
W LDE + L +LP D LLF A + HR +FD NE++L+ L+SIKTG C EDC YC QS
Sbjct: 14 WTLDEALALLDLPDEDELLFEAAQKHRLHFDGNEVQLSTLISIKTGCCPEDCAYCSQSAR 73
Query: 88 YNTEITATKILSIESVITAAQKAKSDGATRFCMGAAWRELKDRDLDNIENMICEVKKI-G 146
Y T + A K++ +E ++ AA+KAK+ GATRFCMGAA R RD++ + I VK+ G
Sbjct: 74 YKTGVKARKLMEVEEILEAAKKAKAAGATRFCMGAAGRG-PGRDMEEVVEAIKAVKEELG 132
Query: 147 LETCLTLGMLNENQAYRLKKVGLDYYNHNLDTSPKLYGDIISTRDYENRLNTLKNVRNVG 206
LE C +LGML E QA +L G+D YNHNL+TSP+ Y +II+TR YE+RLNTL+NVR G
Sbjct: 133 LEVCASLGMLTEEQAEKLADAGVDRYNHNLETSPEFYENIITTRTYEDRLNTLENVREAG 192
Query: 207 INICCGGIIGLSESRDQRAELIFQLANLNPYPESVPINNLVQIKGTPLYGSSILDPLEFI 266
I +C GGI+GL E+ + RAEL+ +LANL P+SVPIN L I GTPL + LDP EF+
Sbjct: 193 IEVCSGGIVGLGETVEDRAELLLELANLPT-PDSVPINFLNPIPGTPLENAKPLDPFEFL 251
Query: 267 RTIAVARITMPTSRIRMSAGRKEMGETTQAFCFLAGANSIFYGDKLLTTDNTKTNDDSKL 326
+TIAVARI MP S IR+SAGR+ M QA F+AGANSIF GDK LTT + D +L
Sbjct: 252 KTIAVARIIMPKSMIRLSAGRETMLPELQALAFMAGANSIFVGDKYLTTPGPDEDKDLEL 311
Query: 327 LKKLGI 332
LK LG+
Sbjct: 312 LKDLGL 317
>gnl|CDD|235755 PRK06256, PRK06256, biotin synthase; Validated.
Length = 336
Score = 272 bits (697), Expect = 8e-90
Identities = 112/304 (36%), Positives = 173/304 (56%), Gaps = 9/304 (2%)
Query: 32 DEVINLFNLP---FNDLLFRAQKVHRKYFDANEIELAVLLSIKTGGCTEDCGYCPQSTHY 88
+E + L +P +LL A +V + + +++L +++ K+G C EDCGYC QS
Sbjct: 23 EEALALLEIPDDDLLELLAAAYEVRKHFCG-KKVKLNTIINAKSGLCPEDCGYCSQSAGS 81
Query: 89 NTEITATKILSIESVITAAQKAKSDGATRFCMGAAWRELKDRDLDNIENMICEVKK-IGL 147
+ + L IE +I AA++A +GA FC+ A+ R +++D + + +K+ L
Sbjct: 82 SAPVYRYAWLDIEELIEAAKEAIEEGAGTFCIVASGRGPSGKEVDQVVEAVKAIKEETDL 141
Query: 148 ETCLTLGMLNENQAYRLKKVGLDYYNHNLDTSPKLYGDIISTRDYENRLNTLKNVRNVGI 207
E C LG+L E QA RLK+ G+D YNHNL+TS + ++++T YE+R++T + V+ GI
Sbjct: 142 EICACLGLLTEEQAERLKEAGVDRYNHNLETSRSYFPNVVTTHTYEDRIDTCEMVKAAGI 201
Query: 208 NICCGGIIGLSESRDQRAELIFQLANLNPYPESVPINNLVQIKGTPLYGSSILDPLEFIR 267
C GGIIG+ ES + R E F L L+ +S+PIN L I GTPL L PLE ++
Sbjct: 202 EPCSGGIIGMGESLEDRVEHAFFLKELD--ADSIPINFLNPIPGTPLENHPELTPLECLK 259
Query: 268 TIAVARITMPTSRIRMSAGRKEMGETTQAFCFLAGANSIFYGDKLLTTDNTKTNDDSKLL 327
TIA+ R+ P IR++ GR E+ + L GANS+ G+ L T T D ++
Sbjct: 260 TIAIFRLINPDKEIRIAGGR-EVNLRSLQPLGLGGANSVIVGNYLTTVGQPAT-ADLDMI 317
Query: 328 KKLG 331
+ LG
Sbjct: 318 EDLG 321
>gnl|CDD|236279 PRK08508, PRK08508, biotin synthase; Provisional.
Length = 279
Score = 183 bits (466), Expect = 6e-56
Identities = 97/276 (35%), Positives = 141/276 (51%), Gaps = 6/276 (2%)
Query: 60 NEIELAVLLSIKTGGCTEDCGYCPQSTHYNTEITATKILSIESVITAAQKAKSDGATRFC 119
EI L + +I +G C EDC YC QS HY +I K IE ++ A+ AK++GA FC
Sbjct: 2 KEIFLCAISNISSGNCKEDCKYCTQSAHYKADIKRYKRKDIEQIVQEAKMAKANGALGFC 61
Query: 120 MGAAWRELKDRDLDNIENMICEVKKIGLETCLTL--GMLNENQAYRLKKVGLDYYNHNLD 177
+ + R L D+ L+ + VKK L G + Q LKK G+ YNHNL+
Sbjct: 62 LVTSGRGLDDKKLEYVAEAAKAVKKEVPGLHLIACNGTASVEQLKELKKAGIFSYNHNLE 121
Query: 178 TSPKLYGDIISTRDYENRLNTLKNVRNVGINICCGGIIGLSESRDQRAELIFQLANLNPY 237
TS + + I +T +E R T +N + G+ +C GGI GL ES + R + LA+L+
Sbjct: 122 TSKEFFPKICTTHTWEERFQTCENAKEAGLGLCSGGIFGLGESWEDRISFLKSLASLS-- 179
Query: 238 PESVPINNLVQIKGTPLYGSSILDPLEFIRTIAVARITMPTSRIRMSAGRKEMGETTQAF 297
P S PIN + PL + L E + + +A+ +P +R+ ++ GR+ + Q
Sbjct: 180 PHSTPINFFIPNPALPLKAPT-LSADEALEIVRLAKEALPNARLMVAGGREVVFGERQYE 238
Query: 298 CFLAGANSIFYGDKLLTTDNTKTNDDSKLLKKLGIN 333
F AGAN+I GD LTT D + LK LG
Sbjct: 239 IFEAGANAIVIGD-YLTTKGEAPKKDIEKLKSLGFE 273
>gnl|CDD|214877 smart00876, BATS, Biotin and Thiamin Synthesis associated domain.
Biotin synthase (BioB), , catalyses the last step of the
biotin biosynthetic pathway. The reaction consists in
the introduction of a sulphur atom into dethiobiotin.
BioB functions as a homodimer. Thiamin synthesis if a
complex process involving at least six gene products
(ThiFSGH, ThiI and ThiJ). Two of the proteins required
for the biosynthesis of the thiazole moiety of thiamine
(vitamin B(1)) are ThiG and ThiH (this entry) and form a
heterodimer. Both of these reactions are thought of
involve the binding of co-factors, and both function as
dimers.. This domain therefore may be involved in
co-factor binding or dimerisation.
Length = 94
Score = 125 bits (316), Expect = 7e-36
Identities = 47/93 (50%), Positives = 61/93 (65%), Gaps = 1/93 (1%)
Query: 242 PINNLVQIKGTPLYG-SSILDPLEFIRTIAVARITMPTSRIRMSAGRKEMGETTQAFCFL 300
PIN L I+GTPL + P EF+RTIA AR+ +P + IR+S GR+ + QA CF
Sbjct: 1 PINRLRPIEGTPLEDPPPPVSPEEFLRTIAAARLALPDAGIRLSTGREALLRDLQALCFS 60
Query: 301 AGANSIFYGDKLLTTDNTKTNDDSKLLKKLGIN 333
AGANSIF GDK LTT ++ DD +L+KLG+
Sbjct: 61 AGANSIFGGDKYLTTSGPRSADDVAMLEKLGLE 93
>gnl|CDD|219245 pfam06968, BATS, Biotin and Thiamin Synthesis associated domain.
Biotin synthase (BioB), EC:2.8.1.6, catalyzes the last
step of the biotin biosynthetic pathway. The reaction
consists in the introduction of a sulphur atom into
dethiobiotin. BioB functions as a homodimer. Thiamin
synthesis if a complex process involving at least six
gene products (ThiFSGH, ThiI and ThiJ). Two of the
proteins required for the biosynthesis of the thiazole
moiety of thiamine (vitamin B(1)) are ThiG and ThiH
(this family) and form a heterodimer. Both of these
reactions are thought of involve the binding of
co-factors, and both function as dimers. This domain
therefore may be involved in co-factor binding or
dimerisation (Finn, RD personal observation).
Length = 93
Score = 111 bits (279), Expect = 2e-30
Identities = 37/92 (40%), Positives = 53/92 (57%)
Query: 242 PINNLVQIKGTPLYGSSILDPLEFIRTIAVARITMPTSRIRMSAGRKEMGETTQAFCFLA 301
PIN L I+GTPL L E ++TIA R+ +P + IR+S GR+ + Q F++
Sbjct: 1 PINFLRPIEGTPLEDQPPLSDEEALKTIAAFRLLLPDAGIRLSGGREALLRDLQGLAFMS 60
Query: 302 GANSIFYGDKLLTTDNTKTNDDSKLLKKLGIN 333
GANS F G L T+ N ++D +LK LG+
Sbjct: 61 GANSTFVGGYLTTSGNRSPDEDIAMLKDLGLE 92
>gnl|CDD|214792 smart00729, Elp3, Elongator protein 3, MiaB family, Radical SAM.
This superfamily contains MoaA, NifB, PqqE,
coproporphyrinogen III oxidase, biotin synthase and MiaB
families, and includes a representative in the
eukaryotic elongator subunit, Elp-3. Some members of the
family are methyltransferases.
Length = 216
Score = 110 bits (278), Expect = 6e-29
Identities = 42/222 (18%), Positives = 79/222 (35%), Gaps = 21/222 (9%)
Query: 66 VLLSIKTGGCTEDCGYCPQSTHYNTEITATKILSIESVITAAQKAKSDGA-----TRFCM 120
+ L I T GC C +C + + +E+++ + G +
Sbjct: 2 LALYIITRGCPRRCTFCSFPSLRGKL----RSRYLEALVREIELLAEKGEKEGLVGTVFI 57
Query: 121 GAAWRELKDRD-----LDNIENMICEVKKIGLETCLTLGMLNENQAYRLKKVGLDYYNHN 175
G L + L+ I ++ K + + L E LK+ G++ +
Sbjct: 58 GGGTPTLLSPEQLEELLEAIREILGLAKDVEITIETRPDTLTEELLEALKEAGVNRVSLG 117
Query: 176 LDT-SPKLYGDIISTRDYENRLNTLKNVRNVG-INICCGGIIGLS-ESRDQRAELIFQLA 232
+ + ++ I E+ L ++ +R G I + I+GL E+ + E + L
Sbjct: 118 VQSGDDEVLKAINRGHTVEDVLEAVELLREAGPIKVSTDLIVGLPGETEEDFEETLKLLK 177
Query: 233 NLNPYPESVPINNLVQIKGTPLYGSSILDPLEFIRTIAVARI 274
L P+ V I L GTPL + L+ A +
Sbjct: 178 ELG--PDRVSIFPLSPRPGTPLA--KMYKRLKPPTKEERAEL 215
>gnl|CDD|217866 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM
proteins catalyze diverse reactions, including unusual
methylations, isomerisation, sulphur insertion, ring
formation, anaerobic oxidation and protein radical
formation.
Length = 165
Score = 74.9 bits (184), Expect = 3e-16
Identities = 41/165 (24%), Positives = 66/165 (40%), Gaps = 10/165 (6%)
Query: 70 IKTGGCTEDCGYCPQSTHYNTEITATKILSIESVITAAQKAKSDGATRFCMG----AAWR 125
I T GC C YC + + LS E ++ A++ G +
Sbjct: 2 IVTRGCNLRCTYCAFPSIRARG--KGRELSPEEILEEAKELARLGVEVVILTGGEPLLLP 59
Query: 126 ELKDRDLDNIENMICEVKKIGLETCLTLGMLNENQAYRLKKVGLDYYNHNLDTSPKLYGD 185
+L + ++ E +I LET TL L+E LK+ GLD + +L +
Sbjct: 60 DLVELLERLLKLREGEGIRITLETNGTL--LDEELLEELKEAGLDRVSISLQSGDDEVLK 117
Query: 186 II-STRDYENRLNTLKNVRNVGINICCGGIIGLS-ESRDQRAELI 228
II +E L L+ +R GI + I+GL E+ + E +
Sbjct: 118 IINRGHTFEEVLEALELLREAGIPVVVDNIVGLPGENDEDLEETL 162
>gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this
family generate radicals by combining a 4Fe-4S cluster
and S-adenosylmethionine (SAM) in close proximity. They
are characterized by a conserved CxxxCxxC motif, which
coordinates the conserved iron-sulfur cluster.
Mechanistically, they share the transfer of a single
electron from the iron-sulfur cluster to SAM, which
leads to its reductive cleavage to methionine and a
5'-deoxyadenosyl radical, which, in turn, abstracts a
hydrogen from the appropriately positioned carbon atom.
Depending on the enzyme, SAM is consumed during this
process or it is restored and reused. Radical SAM
enzymes catalyze steps in metabolism, DNA repair, the
biosynthesis of vitamins and coenzymes, and the
biosynthesis of many antibiotics. Examples are biotin
synthase (BioB), lipoyl synthase (LipA), pyruvate
formate-lyase (PFL), coproporphyrinogen oxidase (HemN),
lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide
reductase (ARR), and MoaA, an enzyme of the
biosynthesis of molybdopterin.
Length = 204
Score = 69.3 bits (169), Expect = 7e-14
Identities = 54/208 (25%), Positives = 88/208 (42%), Gaps = 15/208 (7%)
Query: 72 TGGCTEDCGYC--PQSTHYNTEITATKILSIESVITAAQKAKSDGATRFCMGAAWRELKD 129
T GC +CG+C P S E IE ++ +AK G + L
Sbjct: 4 TRGCNLNCGFCSNPASKGRGPES----PPEIEEILDIVLEAKERGVEVVILTGGEPLLYP 59
Query: 130 RDLDNIENMI--CEVKKIGLETCLTLGMLNENQAYRLKKVGLDYYNHNLDTSPKLYGDII 187
+ + + +I +ET +L E LK++GLD +LD+ + D I
Sbjct: 60 ELAELLRRLKKELPGFEISIET--NGTLLTEELLKELKELGLDGVGVSLDSGDEEVADKI 117
Query: 188 --STRDYENRLNTLKNVRNVGINICCGGIIGLS-ESRDQRAELIFQLANLNPYPESVPIN 244
S ++ RL LK +R G+ + ++GL E + E + LA P+ V +
Sbjct: 118 RGSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEELELLAEFRS-PDRVSLF 176
Query: 245 NLVQIKGTPLYGSSILDPLE-FIRTIAV 271
L+ +GTPL ++ + P E +R IA
Sbjct: 177 RLLPEEGTPLELAAPVVPAEKLLRLIAA 204
>gnl|CDD|188472 TIGR03957, rSAM_HmdB, 5,10-methenyltetrahydromethanopterin
hydrogenase cofactor biosynthesis protein HmdB. Members
of this archaeal protein family are HmdB, a partially
characterized radical SAM protein with an unusual
CX5CX2C motif. Its gene flanks the H2-forming
methylene-H4-methanopterin dehydrogenase gene hmdA,
found in hydrogenotrophic methanogens. HmdB appears to
act in in biosynthesis of the novel cofactor of HmdA
[Protein fate, Protein modification and repair, Energy
metabolism, Methanogenesis].
Length = 317
Score = 62.5 bits (152), Expect = 5e-11
Identities = 72/296 (24%), Positives = 112/296 (37%), Gaps = 42/296 (14%)
Query: 32 DEVINLFN-------LPFNDLLFRAQKVHRKYFDANEIELAVLLSIKTGGC--TEDCGYC 82
DE + LF L D+ R + R +I+L + I T C C YC
Sbjct: 4 DEALKLFKSDNSRDLLKLFDIASRVRDYFRG-----KIKLTSTIHI-TNICHVRPKCLYC 57
Query: 83 -----PQSTHYNTEITATKILSIESVITAAQKAKSDGATRF-CMGAAWRELKDRDLDNIE 136
Y T E + AA+ + G R C GA +
Sbjct: 58 GFAAGTSKEGYYEPFRKTD----EEIKEAAKAIEESGIPRVSCSGAHG--------YGGK 105
Query: 137 NMICEVKKIGLETCLTLGM-----LNENQAYRLKKVGLDYYNHNLDT-SPKLYGDIISTR 190
+ + + T L L + L E L + G D NL+T + +L+ +
Sbjct: 106 EAVRAARIVKENTSLELLINVGADLTEESIEELARYGTDTICCNLETTNEELFKKLKPGE 165
Query: 191 DYENRLNTLKNVRNVGINICCGGIIGLSESRDQRAELIFQLANLNPYPESVPINNLVQIK 250
+ E+R+ + V GI + G +IG+ ES + R E + L E +PI
Sbjct: 166 ELEDRIRVCEMVCKYGIELSSGLLIGIGESYEDRLEHLKFLKRFENLGE-IPIMGFNPYP 224
Query: 251 GTPLYGSSILDPLEFIRTIAVARITMPTSRIRMSAGRKEMGETTQAFCFLAGANSI 306
GTP+ LE +TIAV R+ P IR++ +G F +AGA+++
Sbjct: 225 GTPMENHPPCSLLEQAKTIAVTRLMYPD--IRITVPTPTIGPENVQFALMAGADNV 278
>gnl|CDD|223988 COG1060, ThiH, Thiamine biosynthesis enzyme ThiH and related
uncharacterized enzymes [Coenzyme metabolism / General
function prediction only].
Length = 370
Score = 56.1 bits (136), Expect = 8e-09
Identities = 44/257 (17%), Positives = 83/257 (32%), Gaps = 34/257 (13%)
Query: 75 CTEDCGYCPQSTHYNTEITATKILSIESVITAAQKAKSDGATRFCMGAAWRELKDRDLDN 134
C DC +C LS E ++ ++A G T + E + L+
Sbjct: 69 CVNDCTFCAFYRKPGDP--KAYTLSPEEILEEVREAVKRGITEVLIVGG--EHPELSLEY 124
Query: 135 IENMICEVKKIGLETCLTL-------------GMLNENQAYRLKKVGLDYY-----NHNL 176
E + +K+ + + G+ E RLK+ GLD
Sbjct: 125 YEELFRTIKEEFPDLHIHALSAGEILFLAREGGLSYEEVLKRLKEAGLDSMPGGGAEILS 184
Query: 177 DTSPKLYGDIIS--TRDYENRLNTLKNVRNVGINICCGGIIGLSESRDQRAELIFQLANL 234
+ I + E L + +GI ++G E+R+ R + + + +L
Sbjct: 185 EE----VRKIHCPPKKSPEEWLEIHERAHRLGIPTTATMLLGHVETREDRIDHLEHIRDL 240
Query: 235 N---PYPESVPINNLVQIKGT-PLYGSSILDPLEFIRTIAVARITMPTS-RIRMSAGRKE 289
+ G P + ++ IA+ARI + + ++ +
Sbjct: 241 QDETGGFQEFIPLRFRPENGPLPAEVVPEASLEQDLKAIALARIFLDNNISNIQASWLR- 299
Query: 290 MGETTQAFCFLAGANSI 306
G L+GAN +
Sbjct: 300 DGVILAQAALLSGANDL 316
>gnl|CDD|132589 TIGR03550, F420_cofG, 7,8-didemethyl-8-hydroxy-5-deazariboflavin
synthase, CofG subunit. This model represents either a
subunit or a domain, depending on whether or not the
genes are fused, of a bifunctional protein that
completes the synthesis of
7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is
the chromophore of coenzyme F(420), involved in
methanogenesis in methanogenic archaea but found in
certain other lineages as well. The chromophore also
occurs as a cofactor in DNA photolyases in Cyanobacteria
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 322
Score = 55.8 bits (135), Expect = 9e-09
Identities = 65/258 (25%), Positives = 106/258 (41%), Gaps = 38/258 (14%)
Query: 75 CTEDCGYCPQSTHYNT--EITATKILSIESVITAAQKAKSDGATR--FCMG--------A 122
C CGYC T E+ A +LS E V+ +K + G T F G
Sbjct: 14 CRNRCGYC---TFRRPPGELEAA-LLSPEEVLEILRKGAAAGCTEALFTFGEKPEERYPE 69
Query: 123 AWRELKDRDLDNIENMICEVKKIGLETCLTL-----GMLNENQAYRLKKV----GLDYYN 173
A L + D+ + E+ ++ LE L G+++ ++ RLK V GL
Sbjct: 70 AREWLAEMGYDSTLEYLRELCELALEETGLLPHTNPGVMSRDELARLKPVNASMGLMLET 129
Query: 174 HNLDTSPKLYGDII----STRDYENRLNTLKNVRNVGINICCGGIIGLSESRDQRAELIF 229
TS +L +D RL T+++ + I G +IG+ E+R++RAE +
Sbjct: 130 ----TSERLCKGEAHYGSPGKDPAVRLETIEDAGRLKIPFTTGILIGIGETREERAESLL 185
Query: 230 QLANLNP---YPESVPINNLVQIKGTPLYGSSILDPLEFIRTIAVARITMPTSRIRMSAG 286
+ L+ + + V + N GTP+ E +RT+AVAR+ +P I +
Sbjct: 186 AIRELHERYGHIQEVIVQNFRAKPGTPMENHPEPSLEEMLRTVAVARLILP-PDISIQVP 244
Query: 287 RKEMGETTQAFCFLAGAN 304
E + AG +
Sbjct: 245 PNLNREDYRLL-LDAGID 261
>gnl|CDD|188425 TIGR03910, pyrrolys_PylB, pyrrolysine biosynthesis radical SAM
protein. This model describes a radical SAM protein,
PylB, that is part of the three-gene cassette sufficient
for the biosynthesis of pyrrolysine (the twenty-second
amino acid) when expressed heterologously in E. coli.
The pyrrolysine next is ligated to its own tRNA and
incorporated at special UAG codons [Amino acid
biosynthesis, Other].
Length = 347
Score = 52.1 bits (125), Expect = 2e-07
Identities = 59/250 (23%), Positives = 110/250 (44%), Gaps = 15/250 (6%)
Query: 42 FNDLLFRAQKVHRKYFDANEIELAVLLSIKTGGCTEDCGYCPQSTHYNTEITATKI--LS 99
L + A++V KYF N + L L T C +C +C +Y A + +
Sbjct: 35 MEKLFYVAREVRNKYF-GNRVFLYGFLYFSTF-CKNNCAFC----YYRKSNHAIRRYRKT 88
Query: 100 IESVITAAQKAKSDGA--TRFCMGAAWRELKD-RDLDNIENMICEVKK-IGLETCLTLGM 155
E + AA+ G MG D R + + ++ VK+ GL ++ G+
Sbjct: 89 REEIKAAARALADSGVHLIDLTMGEDPYYHNDPRGFERLAELVRMVKEETGLPVMISPGV 148
Query: 156 LNENQAYRLKKVGLDYYNHNLDTSPK-LYGDIISTRDYENRLNTLKNVRNVGINICCGGI 214
++ +LK+ G ++Y +T + LY + + ++ R+N+ ++ + +G I G +
Sbjct: 149 VDNETLKKLKEAGANWYACYQETHDRELYNKLRVGQSFDERMNSKRHAKRIGYLIEEGIL 208
Query: 215 IGLSESRDQRAELIFQLANLNPYPESVPINNLVQIKGTPLYGSSILDPLEFIRTIAVARI 274
G+ + + A + + +L+ + V + V KGTPL G + L +R IA+ R+
Sbjct: 209 TGVGDDIEDTAISLRGMKSLDA--DQVRVMTFVPQKGTPLEGKDVEGNLAELRIIAIMRL 266
Query: 275 TMPTSRIRMS 284
P I S
Sbjct: 267 LFPDRLIPAS 276
>gnl|CDD|180485 PRK06245, cofG, FO synthase subunit 1; Reviewed.
Length = 336
Score = 47.2 bits (113), Expect = 6e-06
Identities = 56/229 (24%), Positives = 94/229 (41%), Gaps = 32/229 (13%)
Query: 75 CTEDCGYCPQSTHYNTEITATKILSIESVITAAQKAKSDGATR--FCMG--------AAW 124
C CGYC + + +LS E V ++ G T F G
Sbjct: 22 CRNRCGYC----TFRRDPGQPSLLSPEEVKEILRRGADAGCTEALFTFGEVPDESYERIK 77
Query: 125 RELKDRDLDNIENMICEVKKIGLETCL----TLGMLNENQAYRLKKV----GLDYYNHNL 176
+L + +I + ++ ++ LE L G+L + +LK+V GL
Sbjct: 78 EQLAEMGYSSILEYLYDLCELALEEGLLPHTNAGILTREEMEKLKEVNASMGLMLEQ--- 134
Query: 177 DTSPKLYGDIIS---TRDYENRLNTLKNVRNVGINICCGGIIGLSESRDQRAELIFQLAN 233
TSP+L + +D E RL T++N + I G +IG+ E+ + RAE + +A
Sbjct: 135 -TSPRLLNTVHRGSPGKDPELRLETIENAGKLKIPFTTGILIGIGETWEDRAESLEAIAE 193
Query: 234 LNP---YPESVPINNLVQIKGTPLYGSSILDPLEFIRTIAVARITMPTS 279
L+ + + V I N G P+ E +R +A+AR+ +P
Sbjct: 194 LHERYGHIQEVIIQNFSPKPGIPMENHPEPSLEEMLRVVALARLILPPD 242
>gnl|CDD|180835 PRK07094, PRK07094, biotin synthase; Provisional.
Length = 323
Score = 45.6 bits (109), Expect = 2e-05
Identities = 61/259 (23%), Positives = 114/259 (44%), Gaps = 19/259 (7%)
Query: 32 DEVINLFNL----PFNDLLFRAQKVHRKYFDANEIELAVLLSIKTGGCTEDCGYCPQSTH 87
DE++ L + L A +V +KY +E+ L L+ + C +C YC
Sbjct: 4 DEILELLSNDDEEELKYLFKAADEVRKKYVG-DEVHLRGLIEF-SNYCRNNCLYCGLRRD 61
Query: 88 YNTEITATKILSIESVITAAQKAKSDGATRFCM--GAAWRELKDRDLDNIENMICEVKKI 145
N I + LS E ++ A+KA G + G ++ I ++I E+KK
Sbjct: 62 -NKNIERYR-LSPEEILECAKKAYELGYRTIVLQSGEDPYYTDEK----IADIIKEIKKE 115
Query: 146 -GLETCLTLGMLNENQAYRLKKVGLDYYNHNLDTS-PKLYGDIISTRDYENRLNTLKNVR 203
+ L+LG + + K+ G D Y +T+ +LY + +ENR+ LK+++
Sbjct: 116 LDVAITLSLGERSYEEYKAWKEAGADRYLLRHETADKELYAKLHPGMSFENRIACLKDLK 175
Query: 204 NVGINICCGGIIGL-SESRDQRAELIFQLANLNPYPESVPINNLVQIKGTPLYGSSILDP 262
+G + G ++GL ++ + A+ I L L+ + + I + TPL
Sbjct: 176 ELGYEVGSGFMVGLPGQTLEDLADDILFLKELD--LDMIGIGPFIPHPDTPLKDEKGGSL 233
Query: 263 LEFIRTIAVARITMPTSRI 281
++ +A+ R+ +P + I
Sbjct: 234 ELTLKVLALLRLLLPDANI 252
>gnl|CDD|237261 PRK12928, PRK12928, lipoyl synthase; Provisional.
Length = 290
Score = 43.8 bits (104), Expect = 6e-05
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 160 QAYRLKKVGL---DYYNHNLDTSPKLYGDIISTRDYENRLNTLKNVRNVGINIC--CGGI 214
Q RL V D +NHNL+T P+L + DY+ L+ L + + +I G +
Sbjct: 152 QRERLATVLAAKPDVFNHNLETVPRLQKAVRRGADYQRSLDLLARAKELAPDIPTKSGLM 211
Query: 215 IGLSESRDQRAELIFQLANL 234
+GL E+ D E+I L +L
Sbjct: 212 LGLGETED---EVIETLRDL 228
>gnl|CDD|223397 COG0320, LipA, Lipoate synthase [Coenzyme metabolism].
Length = 306
Score = 41.5 bits (98), Expect = 4e-04
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 164 LKKVGLDYYNHNLDTSPKLYGDIISTRDYENRLNTLKNVRNVGINIC--CGGIIGLSESR 221
+ G D +NHN++T P+LY + YE L+ L+ + +G +I G ++GL E+
Sbjct: 168 VADAGPDVFNHNVETVPRLYPRVRPGATYERSLSLLERAKELGPDIPTKSGLMVGLGETD 227
Query: 222 DQ 223
++
Sbjct: 228 EE 229
>gnl|CDD|233002 TIGR00510, lipA, lipoate synthase. This enzyme is an iron-sulfur
protein. It is localized to mitochondria in yeast and
Arabidopsis. It generates lipoic acid, a thiol
antioxidant that is linked to a specific Lys as
prosthetic group for the pyruvate and
alpha-ketoglutarate dehydrogenase complexes and the
glycine-cleavage system. The family shows strong
sequence conservation [Biosynthesis of cofactors,
prosthetic groups, and carriers, Lipoate].
Length = 302
Score = 40.2 bits (94), Expect = 8e-04
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 2/72 (2%)
Query: 164 LKKVGLDYYNHNLDTSPKLYGDIISTRDYENRLNTLKNVRNVGINICC--GGIIGLSESR 221
L D YNHNL+T +L + Y L L+ + N+ G ++GL E+
Sbjct: 162 LLDAPPDVYNHNLETVERLTPFVRPGATYRWSLKLLERAKEYLPNLPTKSGIMVGLGETN 221
Query: 222 DQRAELIFQLAN 233
++ + + L +
Sbjct: 222 EEIKQTLKDLRD 233
>gnl|CDD|132590 TIGR03551, F420_cofH, 7,8-didemethyl-8-hydroxy-5-deazariboflavin
synthase, CofH subunit. This enzyme, together with
CofG, complete the biosynthesis of
7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the
chromophore of coenzyme F420. The chromophore is also
used in cyanobacteria DNA photolyases [Biosynthesis of
cofactors, prosthetic groups, and carriers, Other].
Length = 343
Score = 39.2 bits (92), Expect = 0.002
Identities = 53/266 (19%), Positives = 93/266 (34%), Gaps = 50/266 (18%)
Query: 75 CTEDCGYCPQSTHYNTEITATKILSIESVITAAQKAKSDGATRFCMGAAWRELKDRDLDN 134
C CG+C +LS+E + A +A GAT C+ D D D
Sbjct: 49 CYGGCGFCAFRKRKGD--ADAYLLSLEEIAERAAEAWKAGATEVCIQGGI--HPDLDGDF 104
Query: 135 IENMICEVKKIGLETCL-------------TLGMLNENQAYRLKKVGLDYYNHNLDTSPK 181
+++ VK+ + G+ E RLK+ G LD+ P
Sbjct: 105 YLDILRAVKEEVPGMHIHAFSPMEVYYGARNSGLSVEEALKRLKEAG-------LDSMPG 157
Query: 182 LYGDI-------------ISTRDYENRLNTLKNVRNVGINICCGGIIGLSESRDQRAELI 228
+I +ST ++ + +K +GI + G E+ + + +
Sbjct: 158 TAAEILDDEVRKVICPDKLSTAEW---IEIIKTAHKLGIPTTATIMYGHVETPEHWVDHL 214
Query: 229 FQLANL----NPYPESVPINNLVQIKGTPLYGSSILDP----LEFIRTIAVARITMPTSR 280
L + + E VP+ + PLY + P E ++ A+ARI +
Sbjct: 215 LILREIQEETGGFTEFVPLPFVH--YNAPLYLKGMARPGPTGREDLKVHAIARILLHGLI 272
Query: 281 IRMSAGRKEMGETTQAFCFLAGANSI 306
+ A ++G+ GAN +
Sbjct: 273 DNIQASWVKLGKKLAQVALRCGANDL 298
>gnl|CDD|224101 COG1180, PflA, Pyruvate-formate lyase-activating enzyme
[Posttranslational modification, protein turnover,
chaperones].
Length = 260
Score = 37.3 bits (87), Expect = 0.007
Identities = 36/150 (24%), Positives = 61/150 (40%), Gaps = 20/150 (13%)
Query: 68 LSIKTGGCTEDCGYC--PQSTHYNTEITATKILSIESVITAAQKAKSDGATRFCMG--AA 123
LS+ GC C YC P+ + E++ + +S E ++ A ++S G F G
Sbjct: 38 LSVFLQGCNLRCPYCQNPEISQRGREVSG-EEVSPEVLVDKAFYSESGGGVTFSGGEPTL 96
Query: 124 WRELKDRDLDNIENMICEVKKIGLETCL-TLGMLNENQAYRLKKVGLDYYNHNLD---TS 179
E +++ K+ GL L T G L L + LD LD
Sbjct: 97 QAEF-------ALDLLRAAKERGLHVALDTNGFLPPEALEELLPL-LDAV--LLDLKAFD 146
Query: 180 PKLYGDIISTRDYENRLNTLKNVRNVGINI 209
+LY + D E L L+ + ++G+++
Sbjct: 147 DELYRKLTG-ADNEPVLENLELLADLGVHV 175
>gnl|CDD|224769 COG1856, COG1856, Uncharacterized homolog of biotin synthetase
[Function unknown].
Length = 275
Score = 37.1 bits (86), Expect = 0.008
Identities = 37/147 (25%), Positives = 62/147 (42%), Gaps = 16/147 (10%)
Query: 141 EVKKIGLETCLTL----GMLNENQAYRLKK-----VGLDYYNHNLDTSPKLYGDIISTRD 191
E+K + T L + G ++E+ +LK+ V LD+ N D ++Y S D
Sbjct: 79 ELKALKERTGLLINAHVGFVDESDLEKLKEELVDVVSLDFVGDN-DVIKRVYKLPKSVED 137
Query: 192 YENRLNTLKNVRNVGINICCGGIIGLSESR-DQRAELIFQLANLNPYPESVPINNLVQIK 250
Y L +L ++ GI + IGL + + I L N P+++ + L+
Sbjct: 138 Y---LRSLLLLKENGIRVVPHITIGLDFGKIHGEFKAIDILVNYE--PDALVLVVLIPTP 192
Query: 251 GTPLYGSSILDPLEFIRTIAVARITMP 277
GT + S E I+ + AR P
Sbjct: 193 GTKMGNSPPPPVEEAIKVVKYARKKFP 219
>gnl|CDD|236422 PRK09234, fbiC, FO synthase; Reviewed.
Length = 843
Score = 37.3 bits (87), Expect = 0.013
Identities = 26/91 (28%), Positives = 44/91 (48%), Gaps = 4/91 (4%)
Query: 195 RLNTLKNVRNVGINICCGGIIGLSESRDQRAELIFQLANLNP---YPESVPINNLVQIKG 251
RL L++ + + G +IG+ E+ +RAE +F + L+ + + V + N
Sbjct: 220 RLRVLEDAGRLSVPFTTGILIGIGETLAERAESLFAIRKLHREYGHIQEVIVQNFRAKPD 279
Query: 252 TPLYGSSILDPLEFIRTIAVARITM-PTSRI 281
T + G E + TIAVAR+ + P RI
Sbjct: 280 TAMAGVPDAGLEELLATIAVARLVLGPKMRI 310
>gnl|CDD|224163 COG1242, COG1242, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 312
Score = 35.8 bits (83), Expect = 0.028
Identities = 29/111 (26%), Positives = 48/111 (43%), Gaps = 13/111 (11%)
Query: 191 DYENRLNTLKNVRNVGINICCGGIIGL-SESRDQRAELIFQLANLNPYPESVPINNLVQI 249
D+ ++ +K +R GI +C I GL E+RD+ E +A L + + ++ L +
Sbjct: 166 DFACYVDAVKRLRKRGIKVCTHLINGLPGETRDEMLETAKIVAELG--VDGIKLHPLHVV 223
Query: 250 KGTPL---YGSSILDPL---EFIRTIA-VARITMPT---SRIRMSAGRKEM 290
KGTP+ Y L L E++ + P RI A R +
Sbjct: 224 KGTPMEKMYEKGRLKFLSLEEYVELVCDQLEHLPPEVVIHRITGDAPRDTL 274
>gnl|CDD|233968 TIGR02668, moaA_archaeal, probable molybdenum cofactor biosynthesis
protein A, archaeal. This model describes an archaeal
family related, and predicted to be functionally
equivalent, to molybdenum cofactor biosynthesis protein
A (MoaA) of bacteria (see TIGR02666) [Biosynthesis of
cofactors, prosthetic groups, and carriers,
Molybdopterin].
Length = 302
Score = 35.4 bits (82), Expect = 0.029
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 130 RDLDNIENMICEVKKIGLE--TCLTLGMLNENQAYRLKKVGLDYYNHNLDT-SPKLYGDI 186
+DL I I +K G++ + T G+L E A +LK+ GLD N +LDT P+ Y I
Sbjct: 71 KDLIEI---IRRIKDYGIKDVSMTTNGILLEKLAKKLKEAGLDRVNVSLDTLDPEKYKKI 127
Query: 187 ISTRDYENRLNTLKNVRNVGI 207
+ + +++ + G+
Sbjct: 128 TGRGALDRVIEGIESAVDAGL 148
>gnl|CDD|235493 PRK05481, PRK05481, lipoyl synthase; Provisional.
Length = 289
Score = 34.3 bits (80), Expect = 0.067
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 163 RLKKV---GLDYYNHNLDTSPKLYGDIISTRDYENRLNTLKNVRNVGINIC--CGGIIGL 217
L V D +NHNL+T P+LY + DYE L LK + + I G ++GL
Sbjct: 147 ALLTVLDARPDVFNHNLETVPRLYKRVRPGADYERSLELLKRAKELHPGIPTKSGLMVGL 206
Query: 218 SESRDQ 223
E+ ++
Sbjct: 207 GETDEE 212
>gnl|CDD|234446 TIGR04043, rSAM_MSMEG_0568, radical SAM protein, MSMEG_0568 family.
Members of this protein family are radical SAM proteins
related to MSMEG_0568 from Mycobacterium smegmatis.
Members occur within 8-gene operons in species as
diverse as M. smegmatis, Rhizobium leguminosarum,
Synechococcus elongatus, and Sorangium cellulosum. The
function of the operon is unknown, but similarity of
MSMEG_0568 to some cofactor biosynthesis radical SAM
proteins suggests a similar biosynthetic function
[Unknown function, Enzymes of unknown specificity].
Length = 354
Score = 32.3 bits (74), Expect = 0.32
Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 216 GLSESRDQRAELIFQLANLNPYPESVPINNLVQIKGTPLYGSSILDPLEFIRTIAVARIT 275
GL +S D+ +L ++ YP VP V I GTPL G P F +A +
Sbjct: 270 GLGDSPDELVAGAERLIDMGVYPFVVP---FVPISGTPLEGHPAPSP-AF-----MADVY 320
Query: 276 MPTSRIRMSAGRKEMGETTQAFCFLAGANS 305
P +++ +AG +A C GA S
Sbjct: 321 QPVAKMLRAAGMS--SADIKAGCAKCGACS 348
>gnl|CDD|215236 PLN02428, PLN02428, lipoic acid synthase.
Length = 349
Score = 32.4 bits (74), Expect = 0.34
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 163 RLKKVGLDYYNHNLDTSPKLYGDIISTRD----YENRLNTLKNVRNVGINICCGGII--G 216
+ GLD + HN++T +L + RD Y+ L+ LK+ + + I G
Sbjct: 200 TVATSGLDVFAHNIETVERLQRIV---RDPRAGYKQSLDVLKHAKESKPGLLTKTSIMLG 256
Query: 217 LSESRDQ 223
L E+ ++
Sbjct: 257 LGETDEE 263
>gnl|CDD|99994 cd03825, GT1_wcfI_like, This family is most closely related to the
GT1 family of glycosyltransferases. wcfI in Bacteroides
fragilis has been shown to be involved in the capsular
polysaccharide biosynthesis.
Length = 365
Score = 30.3 bits (69), Expect = 1.4
Identities = 10/27 (37%), Positives = 11/27 (40%), Gaps = 9/27 (33%)
Query: 72 TGGC---------TEDCGYCPQSTHYN 89
TGGC +CG CPQ Y
Sbjct: 90 TGGCHYPGGCDRYKTECGNCPQLGSYP 116
>gnl|CDD|216693 pfam01774, UreD, UreD urease accessory protein. UreD is a urease
accessory protein. Urease pfam00449 hydrolyses urea into
ammonia and carbamic acid. UreD is involved in
activation of the urease enzyme via the
UreD-UreF-UreG-urease complex and is required for urease
nickel metallocenter assembly. See also UreF pfam01730,
UreG pfam01495.
Length = 204
Score = 29.8 bits (68), Expect = 1.6
Identities = 13/47 (27%), Positives = 16/47 (34%), Gaps = 1/47 (2%)
Query: 285 AGRKEMGETTQAFCFLAGANSIFYGDKLLTTDNTKTNDDSKLLKKLG 331
GR MGE F L I +LL D + + D L
Sbjct: 98 LGRPAMGERFA-FGRLRSRLEIRRDGRLLLLDRLRLDPDDAALASPA 143
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit.
The RNA polymerase gamma subunit, encoded by the rpoC1
gene, is found in cyanobacteria and corresponds to the
N-terminal region the beta' subunit, encoded by rpoC, in
other bacteria. The equivalent subunit in plastids and
chloroplasts is designated beta', while the product of
the rpoC2 gene is designated beta''.
Length = 619
Score = 30.3 bits (68), Expect = 1.8
Identities = 29/93 (31%), Positives = 49/93 (52%), Gaps = 18/93 (19%)
Query: 181 KLYGDIISTRDYENRLNTLKNVRNVGINIC--CGGIIGLSESRDQRAELIF-QLANLNPY 237
K++G ++D+E K VR+ GI +C CG + ++ESR +R + + +LA
Sbjct: 54 KIFG---PSKDWECHCGKYKRVRHRGI-VCERCG--VEVTESRVRRHRMGYIKLA----- 102
Query: 238 PESVPINNLVQIKGTPLYGSSILD-PLEFIRTI 269
P+ ++ +KG P Y S +LD PL + I
Sbjct: 103 ---APVTHVWYLKGIPSYVSILLDMPLRDVEQI 132
>gnl|CDD|188646 cd00959, DeoC, 2-deoxyribose-5-phosphate aldolase (DERA) of the
DeoC family. 2-deoxyribose-5-phosphate aldolase (DERA)
of the DeoC family. DERA belongs to the class I
aldolases and catalyzes a reversible aldol reaction
between acetaldehyde and glyceraldehyde 3-phosphate to
generate 2-deoxyribose 5-phosphate. DERA is unique in
catalyzing the aldol reaction between two aldehydes, and
its broad substrate specificity confers considerable
utility as a biocatalyst, offering an environmentally
benign alternative to chiral transition metal catalysis
of the asymmetric aldol reaction.
Length = 203
Score = 29.0 bits (66), Expect = 3.0
Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 98 LSIESVITAAQKAKSDGATRFCMGAAWRELKDRDLDNIENMICEVKKIG--------LET 149
+ E + A++A +DGA M LK D + + I V + LET
Sbjct: 66 TTTEVKVAEAREAIADGADEIDMVINIGALKSGDYEAVYEEIAAVVEACGGAPLKVILET 125
Query: 150 CL 151
L
Sbjct: 126 GL 127
>gnl|CDD|183940 PRK13276, PRK13276, cell wall biosynthesis protein ScdA;
Provisional.
Length = 224
Score = 29.0 bits (65), Expect = 3.5
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 16/60 (26%)
Query: 203 RNVGINICCGGIIGLSESRDQRA-----ELIFQL---------ANLNPYPESVPINNLVQ 248
R+VGI+ CCGG + + + ++ EL+ +L +LNP +V +L+Q
Sbjct: 23 RSVGIDFCCGGQVSIEAASLEKKNVDLNELLQRLNDVEQTNTPGSLNPKFLNVS--SLIQ 80
>gnl|CDD|225314 COG2516, COG2516, Biotin synthase-related enzyme [General
function prediction only].
Length = 339
Score = 29.0 bits (65), Expect = 3.8
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 65 AVLLSIKTGGCTEDCGYCPQS 85
A L++ GGC DC YCPQ+
Sbjct: 31 AYLMTTYPGGCIADCAYCPQA 51
>gnl|CDD|172826 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 669
Score = 29.0 bits (65), Expect = 3.9
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 277 PTSRIRMSAGRKEMGETTQAFCFLAGANSIFYGDKLLTTDNTKTNDDSKLLKKLGINTR 335
P S++ +S G K++GE T NS DK+ T + SKLLK GI +
Sbjct: 497 PFSKLLLSMGIKDLGENTILLLINNNLNSF---DKISTLCQDREFALSKLLKIKGIGEK 552
>gnl|CDD|238115 cd00193, t_SNARE, Soluble NSF (N-ethylmaleimide-sensitive fusion
protein)-Attachment protein (SNAP) REceptor domain;
these alpha-helical motifs form twisted and parallel
heterotetrameric helix bundles; the core complex
contains one helix from a protein that is anchored in
the vesicle membrane (synaptobrevin), one helix from a
protein of the target membrane (syntaxin), and two
helices from another protein anchored in the target
membrane (SNAP-25); their interaction forms a core which
is composed of a polar zero layer, a flanking
leucine-zipper layer acts as a water tight shield to
isolate ionic interactions in the zero layer from the
surrounding solvent.
Length = 60
Score = 26.3 bits (59), Expect = 4.4
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 128 KDRDLDNIENMICEVKKIGLET 149
+D +L+ +E I E+K+I L+
Sbjct: 4 RDEELEQLEASIGELKQIFLDL 25
>gnl|CDD|203647 pfam07488, Glyco_hydro_67M, Glycosyl hydrolase family 67 middle
domain. Alpha-glucuronidases, components of an ensemble
of enzymes central to the recycling of photosynthetic
biomass, remove the alpha-1,2 linked 4-O-methyl
glucuronic acid from xylans. This family represents the
central catalytic domain of alpha-glucuronidase.
Length = 328
Score = 28.7 bits (65), Expect = 4.5
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 301 AGANSIFYGDKLLTTDNTKTNDDSKLLKKLGIN 333
AG SIF+ + L D T+ D ++LL +GIN
Sbjct: 41 AG-ASIFFWNGLPRYDLTRYADYARLLASIGIN 72
>gnl|CDD|237686 PRK14356, glmU, bifunctional N-acetylglucosamine-1-phosphate
uridyltransferase/glucosamine-1-phosphate
acetyltransferase; Provisional.
Length = 456
Score = 28.9 bits (65), Expect = 5.0
Identities = 20/66 (30%), Positives = 25/66 (37%), Gaps = 4/66 (6%)
Query: 238 PESVPINNLVQIKGTPLYGSSILDPLEFIRTIAVARITMPTSRIRMSAGRKEMGETTQAF 297
PESV I I P G+ I P E +AR + S + G T +F
Sbjct: 261 PESVRIGPRATI--EP--GAEIYGPCEIYGASRIARGAVIHSHCWLRDAVVSSGATIHSF 316
Query: 298 CFLAGA 303
L GA
Sbjct: 317 SHLEGA 322
>gnl|CDD|177613 PHA03376, PHA03376, BARF1; Provisional.
Length = 221
Score = 28.5 bits (63), Expect = 5.1
Identities = 17/87 (19%), Positives = 32/87 (36%), Gaps = 11/87 (12%)
Query: 25 QSLIWKLDEVINLFNLPFNDLLFRAQKVHRKYFDANEIELAVLLSIKTGGCTEDCGYCPQ 84
Q LI ++ + PF R +FD + L + + D Y +
Sbjct: 57 QVLIGRMHHDVIFIEWPF-----------RGFFDIHRSANTFFLVVTAANISHDGNYLCR 105
Query: 85 STHYNTEITATKILSIESVITAAQKAK 111
TE+T + LS+ +T + ++
Sbjct: 106 MKLGETEVTKQEHLSVVKPLTLSVHSE 132
>gnl|CDD|202660 pfam03480, SBP_bac_7, Bacterial extracellular solute-binding
protein, family 7. This family of proteins are
involved in binding extracellular solutes for transport
across the bacterial cytoplasmic membrane. This family
includes a C4-dicarboxylate-binding protein and the
sialic acid-binding protein SiaP. The structure of the
SiaP receptor has revealed an overall topology similar
to ATP binding cassette ESR (extracytoplasmic solute
receptors) proteins. Upon binding of sialic acid, SiaP
undergoes domain closure about a hinge region and
kinking of an alpha-helix hinge component.
Length = 285
Score = 28.4 bits (64), Expect = 5.4
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 23 SSQSLIWKLDEVINLFNLPFNDLLFRAQKVHRKYFD 58
S + L + +F+LPF LF ++ + D
Sbjct: 60 PSSAYFAGLVPELGVFDLPF---LFDDEEHLERVLD 92
>gnl|CDD|226187 COG3661, AguA, Alpha-glucuronidase [Carbohydrate transport and
metabolism].
Length = 684
Score = 28.7 bits (64), Expect = 5.6
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 304 NSIFYGDKLLTTDNTKTNDDSKLLKKLGIN 333
SIF+ L ++ + D ++ L +GIN
Sbjct: 169 QSIFFWWNLPGHNDQRMKDYARALASIGIN 198
>gnl|CDD|223960 COG1029, FwdB, Formylmethanofuran dehydrogenase subunit B [Energy
production and conversion].
Length = 429
Score = 28.1 bits (63), Expect = 6.7
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 4/70 (5%)
Query: 87 HYNTEITATKILSIESVITAAQKAKSDGATRFCMGAAWRELKDRDLDNIENMICEVKKIG 146
H + E+ I IE + + AK GA +G K R+++N N+ VK +
Sbjct: 222 HRSEEVAGVPIEEIEELADMMKNAKF-GAIFVGLGLTSSRGKHRNVENAINL---VKDLN 277
Query: 147 LETCLTLGML 156
TL +
Sbjct: 278 EYAKFTLIPM 287
>gnl|CDD|100014 cd00286, Tubulin_FtsZ, Tubulin/FtsZ: Family includes tubulin
alpha-, beta-, gamma-, delta-, and epsilon-tubulins as
well as FtsZ, all of which are involved in polymer
formation. Tubulin is the major component of
microtubules, but also exists as a heterodimer and as a
curved oligomer. Microtubules exist in all eukaryotic
cells and are responsible for many functions, including
cellular transport, cell motility, and mitosis. FtsZ
forms a ring-shaped septum at the site of bacterial cell
division, which is required for constriction of cell
membrane and cell envelope to yield two daughter cells.
FtsZ can polymerize into tubes, sheets, and rings in
vitro and is ubiquitous in eubacteria, archaea, and
chloroplasts.
Length = 328
Score = 28.1 bits (63), Expect = 7.0
Identities = 18/98 (18%), Positives = 37/98 (37%), Gaps = 6/98 (6%)
Query: 1 MSLKIIQSSKESNSIKKNNAISSSQSLIWKLDEVINLFNLPFNDLLFRAQKVHRK-YFDA 59
++ I+ E ++ N+I + +L D ++ + N D+ R + + +
Sbjct: 124 ITFSILPGPDEGVIVRPYNSILTLHTLTEHSDCLVVIDNEALFDICPRPLHIDKPTFDHI 183
Query: 60 NEIELAVLLSIKTGGCTEDCGYCPQSTHYNTEITATKI 97
NE+ LA LS T G E++ +
Sbjct: 184 NEL-LATALSSLT-TPLRFDGS---LNVDLRELSENLV 216
>gnl|CDD|235373 PRK05249, PRK05249, soluble pyridine nucleotide transhydrogenase;
Provisional.
Length = 461
Score = 27.8 bits (63), Expect = 8.9
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 7/33 (21%)
Query: 39 NLPFNDLLFRAQKV-------HRKYFDANEIEL 64
+ F DLL RA V R ++ N ++L
Sbjct: 79 RITFADLLARADHVINKQVEVRRGQYERNRVDL 111
>gnl|CDD|173627 cd05037, PTK_Jak_rpt1, Pseudokinase (repeat 1) domain of the
Protein Tyrosine Kinases, Janus kinases. Protein
Tyrosine Kinase (PTK) family; Janus kinase (Jak)
subfamily; pseudokinase domain (repeat1). The Jak
subfamily is composed of Jak1, Jak2, Jak3, TYK2, and
similar proteins. The PTKc (catalytic domain) family to
which this subfamily belongs, is part of a larger
superfamily that includes the catalytic domains of other
kinases such as protein serine/threonine kinases, RIO
kinases, and phosphoinositide 3-kinase (PI3K). PTKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to tyrosine (tyr) residues in protein substrates.
Jak subfamily proteins are cytoplasmic (or nonreceptor)
tyr kinases containing an N-terminal FERM domain,
followed by a Src homology 2 (SH2) domain, a
pseudokinase domain, and a C-terminal catalytic tyr
kinase domain. The pseudokinase domain shows similarity
to tyr kinases but lacks crucial residues for catalytic
activity and ATP binding. It modulates the kinase
activity of the C-terminal catalytic domain. Most Jaks
are expressed in a wide variety of tissues, except for
Jak3, which is expressed only in hematopoietic cells.
Jaks are crucial for cytokine receptor signaling. They
are activated by autophosphorylation upon
cytokine-induced receptor aggregation, and subsequently
trigger downstream signaling events such as the
phosphorylation of signal transducers and activators of
transcription (STATs). Jaks are also involved in
regulating the surface expression of some cytokine
receptors. The Jak-STAT pathway is involved in many
biological processes including hematopoiesis,
immunoregulation, host defense, fertility, lactation,
growth, and embryogenesis.
Length = 259
Score = 27.8 bits (62), Expect = 9.0
Identities = 11/39 (28%), Positives = 16/39 (41%)
Query: 209 ICCGGIIGLSESRDQRAELIFQLANLNPYPESVPINNLV 247
IC G LS E +Q + P P+ + NL+
Sbjct: 199 ICSNGEEPLSTLSSSEKERFYQDQHRLPMPDCAELANLI 237
>gnl|CDD|223518 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 589
Score = 28.0 bits (63), Expect = 9.9
Identities = 10/39 (25%), Positives = 13/39 (33%), Gaps = 3/39 (7%)
Query: 164 LKKVGLDYYNHNLDTSPKLYGDIISTRDYENRLNTLKNV 202
K G Y L T PK G S ++ L+
Sbjct: 357 YKDFGFTDYEVKLSTRPKFIG---SDEMWDKAEAALREA 392
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
0.318 0.134 0.383
Gapped
Lambda K H
0.267 0.0846 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,936,549
Number of extensions: 1607127
Number of successful extensions: 1481
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1443
Number of HSP's successfully gapped: 62
Length of query: 348
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 250
Effective length of database: 6,590,910
Effective search space: 1647727500
Effective search space used: 1647727500
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 (21.7 bits)
S2: 59 (26.3 bits)