RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14407
(522 letters)
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 241 bits (617), Expect = 7e-73
Identities = 170/536 (31%), Positives = 243/536 (45%), Gaps = 96/536 (17%)
Query: 10 FDHAYLAEPSQFAGLGVRNARIKITAGKGLGGSSAVQNILYQRGTSYDYENFAKL-GYNG 68
++ AY EP N R++ GK LGGSS++ ++Y RG + DY+N+A+L G G
Sbjct: 63 YNWAYETEPEPHMN----NRRMECPRGKVLGGSSSINGMVYIRGNAMDYDNWAELPGLEG 118
Query: 69 WGYDETLKYFVKSEDYRSVIYNESKAVHGTQGYLPVGLFK-NKENNIIREIFETSAQELG 127
W Y + L YF K+E G G P+ + + N + + F + + G
Sbjct: 119 WSYADCLPYFKKAETR----DGGEDDYRGGDG--PLSVTRGKPGTNPLFQAFVEAGVQAG 172
Query: 128 YPCPKDMNDRYVDVGFAELPGMTRYGLRFSAADAYLTPIAGKRTNLYVLKRSKVTKVIIN 187
YP D+N Y GF + G R+SAA AYL P A KR NL ++ + +++
Sbjct: 173 YPRTDDLNG-YQQEGFGPMDRTVTNGRRWSAARAYLDP-ALKRPNLTIVTHALTDRILF- 229
Query: 188 DQNVATGVEYVNSKGETVRVTANKEVILTAGAIANAQLLLLSGIGPKAHLDEVKIPVKQD 247
+ A GVEY G A +EVIL+AGAI + QLL LSGIGP HL E+ IPV D
Sbjct: 230 EGKRAVGVEYER-GGGRETARARREVILSAGAINSPQLLQLSGIGPAEHLKELGIPVVHD 288
Query: 248 LR-VGENLK----LNAQF--TGPVMAFSAPLKRTVYSQEMV-FKYLVNRIGP-LSN---A 295
L VGENL+ + Q+ PV + A LK +++ + ++L G SN A
Sbjct: 289 LPGVGENLQDHLEVYIQYECKQPVSLYPA-LK--WWNKPKIGAEWLFTGTGLGASNHFEA 345
Query: 296 GLWSFTGYIDTLQNTARPDLEIHLLYFQQNDIRNMCKIKRAYDFNDEVQ----TAYVNLN 351
G G+I + P+++ H L IR YD ++ V+ A+V
Sbjct: 346 G-----GFIRSRAGVDWPNIQYHFLPVA---IR--------YDGSNAVKGHGFQAHVGPM 389
Query: 352 KRTDMGVISMSLVNPKSCGKVTLKSADPLAPPCIDTGILSEPEDLATLIRGTDYITRLEQ 411
+ S G V LKSADP A P I +S +D E
Sbjct: 390 R-------------SPSRGSVKLKSADPRAHPSILFNYMSTEQD------------WREF 424
Query: 412 TEAIRLAGGTLMSLNLEACSQYPWRSTH------------SWTCYIRHLTTTTSNPVGTV 459
+AIRL T + A Y R ++ +R T +P T
Sbjct: 425 RDAIRL---TREIMAQPALDPYRGREISPGADVQTDEEIDAF---VREHAETAYHPSCTC 478
Query: 460 MMGNADDPNAVVTPDLKVKGIKGLRVADISVLPNAIITQSDAISYMIGEKCADLVK 515
MG DP AVV P+ +V G++GLRV D S++P +A + MI EK ADL++
Sbjct: 479 KMGT--DPMAVVDPEGRVHGVEGLRVVDASIMPTITNGNLNAPTIMIAEKAADLIR 532
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 229 bits (586), Expect = 1e-68
Identities = 147/520 (28%), Positives = 215/520 (41%), Gaps = 59/520 (11%)
Query: 11 DHAYLAEPSQFAGLGVRNARIKITAGKGLGGSSAVQNILYQRGTSYDYENFAKL-GYNGW 69
Y +R + GK LGGSS++ ++Y RG D++ +A+ G GW
Sbjct: 59 GPRYDWGFRTEPEPHLRGRELAWPRGKVLGGSSSINGMVYVRGHPEDFDAWAQESGAPGW 118
Query: 70 GYDETLKYFVKSEDYRSVIYNESKAVHGTQGYLPVGLFKNKENNIIREIFETSAQELGYP 129
YD+ L YF ++ED V + + HG G P+ + + N I F + ++LG+P
Sbjct: 119 PYDDVLPYFKRAEDLLGVGGQDLRTWHGGGG--PLPVSPPRSPNPIARAFIEAGEQLGFP 176
Query: 130 CPKDMNDRYVDVGFAELPGMTRYGLRFSAADAYLTPIAGKRTNLYVLKRSKVTKVIINDQ 189
D N + GF G R+SAA AYL P KR NL +L ++V ++++ +
Sbjct: 177 TTPDPNGADQE-GFGPYCVTICNGRRWSAARAYLKPAL-KRPNLTLLTGARVRRILL-EG 233
Query: 190 NVATGVEYVNSKGETVRVT-ANKEVILTAGAIANAQLLLLSGIGPKAHLDEVKIPVKQDL 248
+ A GVE G T+ A +EV+L AGAI + +LLLLSGIGP HL E I V L
Sbjct: 234 DRAVGVEVEIGDGGTIETAVAAREVVLAAGAINSPKLLLLSGIGPADHLLEHGIDVVGRL 293
Query: 249 R-VGENLK----LNAQFTGPVMAFSAPLKRTVYSQEMVFKYLVNRIGPLS----NAGLWS 299
VG+NL+ + F + L +YL+ R GP + G
Sbjct: 294 PGVGQNLQDHLEIYVAFEATEPTNDSVLSLFSKLGIGADRYLLTRDGPGATNHFEGGFVR 353
Query: 300 FTGYIDTLQNTARPDLEIHLLYFQQNDIRNMCKIKRAYDFNDEVQTAYVNLNKRTDMGVI 359
PD + H + +
Sbjct: 354 SGP------AGEYPDGQYH------------------------FAPLPLAIRAAGAEHGF 383
Query: 360 SMSLVN--PKSCGKVTLKSADPLAPPCIDTGILSEPEDLATLIRGTDYITRLEQTEAIRL 417
++ + PKS G VTL+S DP P ID LS D A G + +
Sbjct: 384 TLHVGPMRPKSRGSVTLRSPDPDNRPVIDPNYLSAEGDRAIFRAGIRLTREI-------I 436
Query: 418 AGGTLMSLNLEACSQYPWRSTHSWTC-YIRHLTTTTSNPVGTVMMGNADDPNAVV-TPDL 475
L + + P +T IR L T +P+GT MG DP AVV P L
Sbjct: 437 GQPALDARRKAELAPGPRVTTDEDISAAIRFLARTAYHPMGTCRMG--SDPAAVVDDPYL 494
Query: 476 KVKGIKGLRVADISVLPNAIITQSDAISYMIGEKCADLVK 515
+V G++ LRV D SV+P + + + E+ AD +
Sbjct: 495 RVHGLENLRVVDASVMPTSTGVNPNLTIIALAERAADHIL 534
>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase. Choline dehydrogenase
catalyzes the conversion of exogenously supplied choline
into the intermediate glycine betaine aldehyde, as part
of a two-step oxidative reaction leading to the
formation of osmoprotectant betaine. This enzymatic
system can be found in both gram-positive and
gram-negative bacteria. As in Escherichia coli ,
Staphylococcus xylosus , and Sinorhizobium meliloti,
this enzyme is found associated in a transciptionally
co-induced gene cluster with betaine aldehyde
dehydrogenase, the second catalytic enzyme in this
reaction. Other gram-positive organisms have been shown
to employ a different enzymatic system, utlizing a
soluable choline oxidase or type III alcohol
dehydrogenase instead of choline dehydrogenase. This
enzyme is a member of the GMC oxidoreductase family
(pfam00732 and pfam05199), sharing a common
evoluntionary origin and enzymatic reaction with alcohol
dehydrogenase. Outgrouping from this model, Caulobacter
crescentus shares sequence homology with choline
dehydrogenase, yet other genes participating in this
enzymatic reaction have not currently been identified
[Cellular processes, Adaptations to atypical
conditions].
Length = 532
Score = 220 bits (562), Expect = 3e-65
Identities = 155/521 (29%), Positives = 230/521 (44%), Gaps = 55/521 (10%)
Query: 5 LSLSEFDHAYLAEPSQFAGLGVRNARIKITAGKGLGGSSAVQNILYQRGTSYDYENFAK- 63
++ Y EP + N R+ GK LGGSS++ ++YQRG DYE +AK
Sbjct: 52 AGNKRYNWIYETEPEPH----MNNRRVGHARGKVLGGSSSINGMIYQRGNPMDYEKWAKP 107
Query: 64 LGYNGWGYDETLKYFVKSEDYRSVIYNESKAVHGTQGYLPVGLFKNKENNIIREIFETSA 123
G W Y + L Y+ + E + K G G P+ + + +N + + F +
Sbjct: 108 EGMESWDYADCLPYYKRLE----TTFGGEKPYRGHDG--PIKVRRGPADNPLFQAFIEAG 161
Query: 124 QELGYPCPKDMNDRYVDVGFAELPGMTRYGLRFSAADAYLTPIAGKRTNLYVLKRSKVTK 183
E GY D+N + GF + G R SAA AYL P A KR NL V R+ VTK
Sbjct: 162 VEAGYNKTPDVNG-FRQEGFGPMDSTVHNGRRVSAARAYLHP-AMKRPNLEVQTRAFVTK 219
Query: 184 VIINDQNVATGVEYVNSKGETVRVTANKEVILTAGAIANAQLLLLSGIGPKAHLDEVKIP 243
+ + N ATGVE+ G ANKEVIL+AGAI + QLL LSGIG HL E+ I
Sbjct: 220 INF-EGNRATGVEFKKG-GRKEHTEANKEVILSAGAINSPQLLQLSGIGDAEHLRELGIE 277
Query: 244 VKQDLR-VGENLKLNAQF------TGPVMAFSA--PLKRTVYSQEMVFKYLVNRIGPLSN 294
+ L VGENL+ + + PV + + LK+ + +F R G
Sbjct: 278 PRIHLPGVGENLQDHLEVYVQHACKQPVSLYPSLNWLKQPFIGAQWLF----GRKG-AGA 332
Query: 295 AGLWSFTGYIDTLQNTARPDLEIHLLYFQQNDIRNMCKIKRAYDFNDEVQTAYVNLNKRT 354
+ + G++ + + P+++ H L + K +A+ F V Y
Sbjct: 333 SNHFEGGGFVRSNDDVDYPNIQYHFLPVAIR--YDGTKAPKAHGFQVHVGPMY------- 383
Query: 355 DMGVISMSLVNPKSCGKVTLKSADPLAPPCIDTGILSEPEDLATLIRGTDYITRLEQTEA 414
S G V +KS DP P I +S ED + + +A
Sbjct: 384 -----------SNSRGHVKIKSKDPFEKPEIVFNYMSHEEDWREFREAIRVTREILKQKA 432
Query: 415 IRLAGGTLMSLNLEACSQYPWRSTHSWTCYIRHLTTTTSNPVGTVMMGNADDPNAVVTPD 474
+ G +S E ++ ++R T +P GT MG A D +VV P+
Sbjct: 433 LDPYRGGEISPGPEV------QTDEEIDEFVRRHGETALHPCGTCKMGPASDEMSVVDPE 486
Query: 475 LKVKGIKGLRVADISVLPNAIITQSDAISYMIGEKCADLVK 515
+V G++GLRV D S++P +A M+GEK AD+++
Sbjct: 487 TRVHGMEGLRVVDASIMPRITNGNLNAPVIMMGEKAADIIR 527
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 168 bits (428), Expect = 2e-46
Identities = 140/492 (28%), Positives = 195/492 (39%), Gaps = 85/492 (17%)
Query: 29 ARIKITAGKGLGGSSAVQNILYQRGTSYDYENFAKLGYNGWGYDETLKYFVKSEDYRSVI 88
I G+ LGGS AV + R D++ + GW +D+ L +F E
Sbjct: 74 RASAIVRGRVLGGSGAVNGGYFCRALPADFDAWPI---PGWSWDDVLPHFRAIETDLDF- 129
Query: 89 YNESKAVHGTQGYLPVGLFKNKENNIIREIFETSAQELGYPCPKDMNDRYVDVGF--AEL 146
+HGT G +PV + E + I F +A G+ D+N D +
Sbjct: 130 ---DGPLHGTAGPIPVR--RTAELDGISAAFVAAALGAGFGWIADLNGSGPDAPTGVGAV 184
Query: 147 PGMTRYGLRFSAADAYLTPIAGKRTNLYVLKRSKVTKVIINDQNVATGVEYVNSKGETVR 206
P G R S A AYL P A KR NL V ++V +++ + A GVE + G
Sbjct: 185 PLNVDGGRRVSTAVAYLLP-ALKRPNLTVEADTRVVRILFS-GTRAVGVEVL-GDGGPRT 241
Query: 207 VTANKEVILTAGAIANAQLLLLSGIGPKAHLDEVKIPVKQDLRVGENLKLNAQFTGPVMA 266
+ A++ V+L AGA+ +A LLLLSGIGP L I V DL VG +
Sbjct: 242 LRADR-VVLCAGAVESAHLLLLSGIGPAEQLRAAGIAVVLDLPVGSD------------- 287
Query: 267 FSAPLKRTVYSQEMVFKYLVNRIGPLSNAGLWSFTGYIDTLQNTARPDLEIHLLYFQQND 326
V E V Y R P + ++T+ NTA D+EI
Sbjct: 288 -------FVDHPEWVLPY---RWRP--THDRPDTSPVLETVLNTA--DIEI--------- 324
Query: 327 IRNMCKIKRAY--DFNDEVQTAYVNLNKRTDMGVISMSLVNPKSCGKVTLKSADPLAPPC 384
R Y F V D + ++L+ P S G++ L SADP PP
Sbjct: 325 --------RPYTAGFTALVP------GSPRDDPHLGVALMRPHSRGRIRLASADPADPPR 370
Query: 385 IDTGILSEPEDLATLIRGTDYITRLEQTEAIRLAGGTLMSLNLEACSQYP--WRSTHSWT 442
I+ S D A L G L L L L A + W T
Sbjct: 371 IEHRYDSSAADRAALRAGAALAHEL-------LGSPELGPLLEPAVREGEASWVLARLAT 423
Query: 443 CYIRHLTTTTSNPVGTVMMGNADDPNAVVTPDLKVKGIKGLRVADISVLPNAIITQSDAI 502
+HL G+ MG DDP AVV +V+G++GL V D S+LP A
Sbjct: 424 S--QHLC-------GSCRMGGRDDPGAVVDARCRVRGVEGLWVVDGSILPVIPSRGPHAT 474
Query: 503 SYMIGEKCADLV 514
+ M+ E+ A+ +
Sbjct: 475 AVMVAERAAEFL 486
>gnl|CDD|218493 pfam05199, GMC_oxred_C, GMC oxidoreductase. This domain found
associated with pfam00732.
Length = 139
Score = 115 bits (291), Expect = 1e-30
Identities = 51/145 (35%), Positives = 67/145 (46%), Gaps = 6/145 (4%)
Query: 366 PKSCGKVTLKSADPLAPPCIDTGILSEPEDLATLIRGTDYITRLEQTEAIRLAGGTLMSL 425
P+S G+VTL S+DPL P ID LS+P DLA L R+ + A L
Sbjct: 1 PRSRGRVTLSSSDPLGLPVIDPNYLSDPADLAALRAALRLARRI-----LAAALVELTPG 55
Query: 426 NLEACSQYPWRSTHSWTCYIRHLTTTTSNPVGTVMMGNADDPNAVVTPDLKVKGIKGLRV 485
+E S YIR T+ +P+GT MG D VV PDL+V G+ LRV
Sbjct: 56 PVEVVPGAAEASDDEILEYIRAAAVTSWHPMGTCRMGADPDD-GVVDPDLRVHGVDNLRV 114
Query: 486 ADISVLPNAIITQSDAISYMIGEKC 510
D SV P++ Y + E+
Sbjct: 115 VDASVFPSSPSGNPTLTIYALAERA 139
>gnl|CDD|216089 pfam00732, GMC_oxred_N, GMC oxidoreductase. This family of
proteins bind FAD as a cofactor.
Length = 218
Score = 115 bits (289), Expect = 2e-29
Identities = 73/237 (30%), Positives = 106/237 (44%), Gaps = 41/237 (17%)
Query: 26 VRNARIKITAGKGLGGSSAVQNILYQRGTSYDYENFAKL-GYNGWGYDETLKYFVKSEDY 84
V R+ + AG +GG S+V R + + +A G GWGYD+ L Y K E
Sbjct: 14 VNGRRMILPAGSTVGGGSSVNWSACIRTPAAVLDEWASEFGLEGWGYDDYLPYMDKVE-- 71
Query: 85 RSVIYNESKAVHGTQGYLPVGLFKNKENNIIREIFETSAQELGYP---CPKDMNDRYVDV 141
G G G+ ++ N + + +A+ELGYP P++ N +
Sbjct: 72 ------------GPLGVTTKGIEESPLNQALLK----AAEELGYPVEAVPRNSNGCH-YC 114
Query: 142 GFAELPGMTRYGLRFSAADAYLTPIAGKRTNLYVLKRSKVTKVIINDQN-VATGVEYVNS 200
GF L G + S A +L P + NL +L +K K+II + A GVE +
Sbjct: 115 GFCGLG--CPTGAKQSTARTWLRPALER--NLRILTGAKAEKIIILGRGGRAVGVEARDG 170
Query: 201 KGETVR-VTANKEVILTAGAIANAQLLLLSGIGPKAHLDEVKIPVKQDLRVGENLKL 256
G R +TA KEV++ AGA+ LLL SG+G H VG+NL+L
Sbjct: 171 GGGIKRLITAAKEVVVAAGALNTPPLLLRSGLGKNPH------------PVGKNLQL 215
>gnl|CDD|215420 PLN02785, PLN02785, Protein HOTHEAD.
Length = 587
Score = 82.5 bits (204), Expect = 1e-16
Identities = 96/381 (25%), Positives = 154/381 (40%), Gaps = 51/381 (13%)
Query: 151 RYGLRFSAADAYLTPIAGKRTNLYVLKRSKVTKVIINDQNV---ATGVEYVNSKGETVR- 206
+G R +AA+ AG L VL + V K++ + ATGV + + G +
Sbjct: 216 EFGRRHTAAELL---AAGNPNKLRVLLHATVQKIVFDTSGKRPRATGVIFKDENGNQHQA 272
Query: 207 -VTANK--EVILTAGAIANAQLLLLSGIGPKAHLDEVKIPVKQDLRVGENLKLNAQFTGP 263
++ NK E+IL+AGAI + Q+LLLSGIGPK L + KIPV L+ + G
Sbjct: 273 FLSNNKGSEIILSAGAIGSPQMLLLSGIGPKKELKKHKIPV----------VLHNEHVGK 322
Query: 264 VMAFSAPLKRT-VYSQEMVFKYLVNRIGPLSNAGLWSFTGYIDTLQNTARPDLEIHLLY- 321
MA P+ V S+ V + L+ +G ++ G+ YI+ + IH +
Sbjct: 323 GMA-DNPMNSIFVPSKAPVEQSLIQTVG-ITKMGV-----YIEASSGFGQSPDSIHCHHG 375
Query: 322 FQQNDIRNMCKIKRAYDFNDEVQTAYVNLNKRT-----DMGVISMSLVNPKSCGKVTLKS 376
+I + I + +Q AY++ K + G I + P S G ++L +
Sbjct: 376 IMSAEIGQLSTIPPKQRTPEAIQ-AYIHRKKNLPHEAFNGGFILEKIAGPISTGHLSLIN 434
Query: 377 ADPLAPPCIDTGILSEPEDLATLIRGTDYITRLEQTEAIR---LAGGTLMS--LNLEACS 431
+ P + P+DL + G I ++ +T M LN+ +
Sbjct: 435 TNVDDNPSVTFNYFKHPQDLQRCVYGIRTIEKIVKTNHFTNFTQCDKQTMEKVLNMSVKA 494
Query: 432 QYPWRSTH-----SWTCYIRHLTTTTSNPVGTVMMGNADDPNAVVTPDLKVKGIKGLRVA 486
H S + + T + G +G VV + KV G+ LRV
Sbjct: 495 NINLIPKHTNDTKSLEQFCKDTVITIWHYHGGCHVGK------VVDQNYKVLGVSRLRVI 548
Query: 487 DISVLPNAIITQSDAISYMIG 507
D S + T A M+G
Sbjct: 549 DGSTFDESPGTNPQATVMMMG 569
>gnl|CDD|233583 TIGR01813, flavo_cyto_c, flavocytochrome c. This model describes a
family of redox proteins related to the succinate
dehydrogenases and fumarate reductases of E. coli,
mitochondria, and other well-characterized systems. A
member of this family from Shewanella frigidimarina
NCIMB400 is characterized as a water-soluble periplasmic
protein with four heme groups, a non-covalently bound
FAD, and essentially unidirectional fumarate reductase
activity. At least seven distinct members of this family
are found in Shewanella oneidensis, a species able to
use a wide variety of pathways for respiraton [Energy
metabolism, Electron transport].
Length = 439
Score = 34.2 bits (79), Expect = 0.16
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 178 RSKVTKVIINDQNVATGVEYVNSKGETVRVTANKEVILTAGAIA 221
SKV +I +DQ GV V KG+ + + A K V+L G
Sbjct: 150 NSKVEDLIQDDQGTVVGVV-VKGKGKGIYIKAAKAVVLATGGFG 192
>gnl|CDD|131515 TIGR02462, pyranose_ox, pyranose oxidase. Pyranose oxidase (also
called glucose 2-oxidase) converts D-glucose and
molecular oxygen to 2-dehydro-D-glucose and hydrogen
peroxide. Peroxide production is believed to be
important to the wood rot fungi in which this enzyme is
found for lignin degradation.
Length = 544
Score = 33.7 bits (77), Expect = 0.25
Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 160 DAYLTPIAGKRTNLYVLKRSKVTKVIINDQN----VATGVEYVNSKGETVRVTANKEVIL 215
+R L L + T+++ N+ N A V + S G+ + A +L
Sbjct: 218 LQPNDDAPSERFTL--LTNHRCTRLVRNETNESEIEAALVRDLLS-GDRFEIKA-DVYVL 273
Query: 216 TAGAIANAQLLLLSGIGPKAHLDEVKIP 243
GA+ N Q+L+ SG G D P
Sbjct: 274 ACGAVHNPQILVNSGFGQLGRPDPTNPP 301
>gnl|CDD|216176 pfam00890, FAD_binding_2, FAD binding domain. This family includes
members that bind FAD. This family includes the
flavoprotein subunits from succinate and fumarate
dehydrogenase, aspartate oxidase and the alpha subunit
of adenylylsulphate reductase.
Length = 401
Score = 33.0 bits (76), Expect = 0.37
Identities = 27/95 (28%), Positives = 41/95 (43%), Gaps = 10/95 (10%)
Query: 178 RSKVTKVIINDQNVATGVEYVN-SKGETVRVTANKEVILTAGAI-ANAQLLLLSGI---- 231
R +I+ D TGV N G VR+ A V+L G NA+LLL +
Sbjct: 160 RHPADDLIVEDG-RVTGVVVENRRNGREVRIRAIAGVLLATGGFGRNAELLLPAAGYADT 218
Query: 232 -GPKAHL-DEVKIPVKQDLRVGENLKLNAQFTGPV 264
GP A+ D + + ++ + ++L QF P
Sbjct: 219 TGPPANTGDGIALALRAGAALTDDLMEFVQF-HPT 252
>gnl|CDD|233368 TIGR01350, lipoamide_DH, dihydrolipoamide dehydrogenase. This
model describes dihydrolipoamide dehydrogenase, a
flavoprotein that acts in a number of ways. It is the E3
component of dehydrogenase complexes for pyruvate,
2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can
also serve as the L protein of the glycine cleavage
system. This family includes a few members known to have
distinct functions (ferric leghemoglobin reductase and
NADH:ferredoxin oxidoreductase) but that may be
predicted by homology to act as dihydrolipoamide
dehydrogenase as well. The motif GGXCXXXGCXP near the
N-terminus contains a redox-active disulfide.
Length = 460
Score = 32.2 bits (74), Expect = 0.61
Identities = 28/84 (33%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 169 KRTNLYVLKRSKVTKVIINDQNVATGVEYVNSKGETVRVTANKEVILTAGAIANAQLLLL 228
K+ + +L +KVT V ND V Y N GET +T K V++ G N + L L
Sbjct: 222 KKKGVKILTNTKVTAVEKNDD----QVTYENKGGETETLTGEK-VLVAVGRKPNTEGLGL 276
Query: 229 SGIGPKAHLDEVK-IPVKQDLRVG 251
+G + LDE I V + +R
Sbjct: 277 EKLGVE--LDERGRIVVDEYMRTN 298
>gnl|CDD|223108 COG0029, NadB, Aspartate oxidase [Coenzyme metabolism].
Length = 518
Score = 32.2 bits (74), Expect = 0.75
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 167 AGKRTNLYVLKRSKVTKVIINDQNVATGVEYVNSKGETVRVTANKEVILTAGAIAN 222
R N+ VL+ ++ +II D GV +N GE A K V+L G +
Sbjct: 143 VRNRPNITVLEGAEALDLIIEDGIGVAGVLVLNRNGELGTFRA-KAVVLATGGLGG 197
>gnl|CDD|183248 PRK11636, mrcA, penicillin-binding protein 1a; Provisional.
Length = 850
Score = 32.0 bits (73), Expect = 0.89
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 5/38 (13%)
Query: 253 NLKLNAQFTGPVMAFSAPLKRTVYSQEMVFKYLVNRIG 290
+ + A + P +AFSAP Y EMV + + NR G
Sbjct: 245 SEPIVANYHAPEIAFSAP-----YLSEMVRQEMYNRYG 277
>gnl|CDD|133214 cd05083, PTKc_Chk, Catalytic domain of the Protein Tyrosine Kinase,
Csk homologous kinase. Protein Tyrosine Kinase (PTK)
family; Csk homologous kinase (Chk); catalytic (c)
domain. The PTKc family 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. Csk
subfamily kinases are cytoplasmic (or nonreceptor) tyr
kinases containing the Src homology domains, SH3 and
SH2, N-terminal to the catalytic tyr kinase domain. They
negatively regulate the activity of Src kinases that are
anchored to the plasma membrane. Chk is also referred to
as megakaryocyte-associated tyrosine kinase (Matk). To
inhibit Src kinases, Chk is translocated to the membrane
via binding to specific transmembrane proteins,
G-proteins, or adaptor proteins near the membrane. Chk
inhibit Src kinases using a noncatalytic mechanism by
simply binding to them. As a negative regulator of Src
kinases, Chk may play important roles in cell
proliferation, survival, and differentiation, and
consequently, in cancer development and progression. Chk
is expressed in brain and hematopoietic cells. Studies
in mice reveal that Chk is not functionally redundant
with Csk and that it plays an important role as a
regulator of immune responses. Chk also plays a role in
neural differentiation in a manner independent of Src by
enhancing Mapk activation via Ras-mediated signaling.
Length = 254
Score = 31.1 bits (70), Expect = 1.1
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 190 NVATGVEYVNSKGETVRVTANKEVILTAGAIANAQLLLLSGIGPKAHLDEVKIPVK 245
+VA G+EY+ SK R A + ++++ +A L+ +G +D K+PVK
Sbjct: 108 DVAEGMEYLESKKLVHRDLAARNILVSEDGVAKVSDFGLARVGSMG-VDNSKLPVK 162
>gnl|CDD|100027 cd00396, PurM-like, AIR (aminoimidazole ribonucleotide) synthase
related protein. This family includes Hydrogen
expression/formation protein HypE, AIR synthases, FGAM
(formylglycinamidine ribonucleotide) synthase and
Selenophosphate synthetase (SelD). The N-terminal domain
of AIR synthase forms the dimer interface of the
protein, and is suggested as a putative ATP binding
domain.
Length = 222
Score = 31.2 bits (71), Expect = 1.1
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 191 VATGVEYVNSKGETVRVTANKEVILTAGAIANAQLLLLSGIGPKAHLDEVKIPVKQDLRV 250
+ TGV+ V V A ++ T G + L G A +D IP+ + +R
Sbjct: 119 ILTGVDAVLELVAAGDVHAMHDI--TDGGLLGTLPELAQASGVGAEIDLEAIPLDEVVRW 176
Query: 251 G 251
Sbjct: 177 L 177
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and conversion].
Length = 562
Score = 31.2 bits (71), Expect = 1.5
Identities = 11/53 (20%), Positives = 21/53 (39%)
Query: 169 KRTNLYVLKRSKVTKVIINDQNVATGVEYVNSKGETVRVTANKEVILTAGAIA 221
K + + + V ++++D GV + + + V K VIL G
Sbjct: 150 KFSGIEIFDEYFVLDLLVDDGGGVAGVVARDLRTGELYVFRAKAVILATGGAG 202
>gnl|CDD|234887 PRK01001, PRK01001, putative inner membrane protein translocase
component YidC; Provisional.
Length = 795
Score = 30.9 bits (70), Expect = 1.8
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 8/37 (21%)
Query: 88 IYNESKAVHGT--------QGYLPVGLFKNKENNIIR 116
I N+ A++GT GYLP+G++ +KE +
Sbjct: 165 ISNKDSAIYGTALVFLRSGNGYLPLGIYNSKEECLES 201
>gnl|CDD|233569 TIGR01776, TonB-tbp-lbp, TonB-dependent lactoferrin and transferrin
receptors. This family of TonB-dependent receptors are
responsible for import of iron from the mammalian iron
carriers lactoferrin and transferrin across the outer
membrane. These receptors are found only in bacteria
which can infect mammals such as Moraxella, Mannheimia,
Neisseria, Actinobacillus, Pasteurella, Haemophilus and
Histophilus species [Transport and binding proteins,
Cations and iron carrying compounds, Transport and
binding proteins, Porins].
Length = 932
Score = 30.9 bits (70), Expect = 2.2
Identities = 30/158 (18%), Positives = 49/158 (31%), Gaps = 26/158 (16%)
Query: 23 GLGVRNARIKITAGKGLGGSSAVQNILYQRGTSYDYENFAKLGYN--------------G 68
GLG R + + L S +N+ + G F L Y G
Sbjct: 606 GLGGRYDKHNFKSTDRLVYSGTYRNLSWNFGIVVKPTPFFSLSYRASTGFRVPSFYELYG 665
Query: 69 WGYDETLK----YFVKSEDYRS--VIYNESKAV-HGTQGYLPVGLFKNKENNIIREIFET 121
+ K F+++ D + + +E A G G+L V F+N+ ++I E
Sbjct: 666 ERRGKASKKNVQQFLRTPDLKPEKSLNHEIGARFKGDFGHLEVSYFRNRYKDMIAE---- 721
Query: 122 SAQELGYPCPKDMNDRYVDVGFAELPGMTRYGLRFSAA 159
A E Y D + G+
Sbjct: 722 -APETRTDNEAGQTYGYCDHNYHNAQNAVLKGINILGK 758
>gnl|CDD|180854 PRK07121, PRK07121, hypothetical protein; Validated.
Length = 492
Score = 30.6 bits (70), Expect = 2.3
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 179 SKVTKVIINDQNVATGVEYVNSKGETVRVTANKEVILTAG 218
++ T++I++D GVE GETV + A K V+L AG
Sbjct: 198 TRATRLIVDDDGRVVGVE-ARRYGETVAIRARKGVVLAAG 236
>gnl|CDD|180419 PRK06134, PRK06134, putative FAD-binding dehydrogenase; Reviewed.
Length = 581
Score = 28.9 bits (65), Expect = 7.4
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 179 SKVTKVIINDQNVATGVEYVNSKGETVRVTANKEVILTAGAIAN 222
+ +++ D VA V V + G + A K V+L AG +
Sbjct: 238 APARELLREDGRVAGAV--VETPGGLQEIRARKGVVLAAGGFPH 279
>gnl|CDD|238990 cd02033, BchX, Chlorophyllide reductase converts chlorophylls into
bacteriochlorophylls by reducing the chlorin B-ring.
This family contains the X subunit of this three-subunit
enzyme. Sequence and structure similarity between bchX,
protochlorophyllide reductase L subunit (bchL and chlL)
and nitrogenase Fe protein (nifH gene) suggest their
functional similarity. Members of the BchX family serve
as the unique electron donors to their respective
catalytic subunits (bchN-bchB, bchY-bchZ and nitrogenase
component 1). Mechanistically, they hydrolyze ATP and
transfer electrons through a Fe4-S4 cluster.
Length = 329
Score = 28.8 bits (64), Expect = 8.2
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 10/44 (22%)
Query: 36 GKGLGGSSAVQNILYQRGTSYDYENFAKLGYNGWGYDETLKYFV 79
G+G GG RG + +E KLG++ W +D L F+
Sbjct: 123 GRGCGG----------RGIIHGFELLEKLGFHDWDFDYVLLDFL 156
>gnl|CDD|153085 cd01676, RNR_II_monomer, Class II ribonucleotide reductase,
monomeric form. Ribonucleotide reductase (RNR)
catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophage, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class II RNRs are found in bacteria that
can live under both aerobic and anaerobic conditions.
Many, but not all members of this class, are found to be
homodimers. This particular subfamily is found to be
active as a monomer. Adenosylcobalamin interacts
directly with an active site cysteine to form the
reactive cysteine radical.
Length = 658
Score = 28.6 bits (64), Expect = 9.2
Identities = 26/111 (23%), Positives = 44/111 (39%), Gaps = 24/111 (21%)
Query: 299 SFTGYIDTLQNTARPDLEIHLLYFQQNDIRNMCKI--KRAYDFNDEV-QTAYVNL-NKRT 354
S +G D + A DL +H D++ I + Y +++ + + + L K T
Sbjct: 420 SMSGIADFIVR-AGGDLTLH-------DLKRWRNIGYEAVYQYDERLSKWLGIPLSIKVT 471
Query: 355 DM---GVISM------SLVNPKSC---GKVTLKSADPLAPPCIDTGILSEP 393
+ G IS+ + P ++ + DPLAP I G EP
Sbjct: 472 CVKPSGTISLLAGASPGMHYPLGKYLIRRIRFQKHDPLAPALIAAGYHVEP 522
>gnl|CDD|237208 PRK12795, fliM, flagellar motor switch protein FliM; Reviewed.
Length = 388
Score = 28.5 bits (64), Expect = 9.5
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 235 AHLDEVKIPVKQ--DLRVGENLKLNAQFTGPV 264
A LDE +P+K+ +L+VG+ L L+A+ V
Sbjct: 308 AVLDEQTLPLKRVLNLKVGDTLMLDARPDALV 339
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 0.134 0.390
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,043,953
Number of extensions: 2524211
Number of successful extensions: 1889
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1863
Number of HSP's successfully gapped: 37
Length of query: 522
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 421
Effective length of database: 6,457,848
Effective search space: 2718754008
Effective search space used: 2718754008
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: 61 (27.3 bits)