Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate 350675 BT1147 glycine dehydrogenase [decarboxylating] (NCBI ptt file)
Query= reanno::WCS417:GFF4367
(946 letters)
>lcl|FitnessBrowser__Btheta:350675 BT1147 glycine dehydrogenase
[decarboxylating] (NCBI ptt file)
Length = 949
Score = 969 bits (2505), Expect = 0.0
Identities = 501/936 (53%), Positives = 646/936 (69%), Gaps = 14/936 (1%)
Query: 13 ARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLSEAEALAKIKAIA 72
+RHIG +ED ML +G DSL+ L IP +I+ L L L+E E I +A
Sbjct: 8 SRHIGINEEDTAVMLRKIGVDSLDELINKTIPANIRLKEPLALAKPLTEYEFGKHIADLA 67
Query: 73 GKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLIS 132
KN+L+ TYIG G+YN TP+ I RN+ ENP WYT+YTPYQ E+SQGRLEAL+NFQT +
Sbjct: 68 SKNKLYTTYIGLGWYNTITPAVIQRNVFENPVWYTSYTPYQTEVSQGRLEALMNFQTAVC 127
Query: 133 DLTGLPIANASLLDEATAAAEAMTFC----KRLSKNKGSNAFFASIHSHPQTLDVLRTRA 188
DLT +P+AN SLLDEATAAAEA+T R + G+N F + PQTL V+ TRA
Sbjct: 128 DLTAMPLANCSLLDEATAAAEAVTMMYALRSRTQQKAGANVVFVDENIFPQTLAVMTTRA 187
Query: 189 EPLGIDVVVGDERELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHGLVAVAADLLA 248
P GI++ VG +E F +LQYP S+G+V DY + T++ H A VAVAAD+L+
Sbjct: 188 IPQGIELRVGKYKEFEPSPEIFACILQYPNSSGNVEDYADFTKKAHEADCKVAVAADILS 247
Query: 249 LTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGK 308
L LLTPPGE+GAD+ G+ QR G P+ +GGP A YF+T+D +KR+MPGR++G S D++GK
Sbjct: 248 LALLTPPGEWGADIVFGTTQRLGTPMFYGGPSAGYFATRDEYKRNMPGRIIGWSKDKYGK 307
Query: 309 PALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARRVHQLTAIL 368
R+A+QTREQHI+REKATSNICTAQ LLA +A YAVYHG +G+ IA R+H +T L
Sbjct: 308 LCYRMALQTREQHIKREKATSNICTAQALLATMAGFYAVYHGQEGIKTIASRIHSITVFL 367
Query: 369 AKGLTALGQNVEQAHFFDTLTLNTGANTAA--VHDKARAQRINLRVVDAERVGVSVDETT 426
K L G A +FDTL + +A + A ++ +NLR + VG S+DETT
Sbjct: 368 DKQLKKFGYTQVNAQYFDTLRFELPEHVSAQQIRTIALSKEVNLRYYENGDVGFSIDETT 427
Query: 427 TQADIETLWAIFA-----DGKALPDFAAQVESTLPAALLRQSPVLSHPVFNRYHSETELM 481
A L +IFA D + + D + S + AL R +P L+H VF+ YH+ETE+M
Sbjct: 428 DIAATNVLLSIFAIAAGKDYQKVEDVPEK--SNIDKALKRTTPFLTHEVFSNYHTETEMM 485
Query: 482 RYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYLELT 541
RY+++L KD++L ++MI LGSCTMKLNAA+EM+P++ EF ++HP P +Q+ GY EL
Sbjct: 486 RYIKRLDRKDISLAQSMISLGSCTMKLNAAAEMLPLSRPEFMSMHPLVPEDQAEGYRELI 545
Query: 542 SDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHGTNP 601
S+L L TG+ +SLQPN+G+ GEYAGL IRAY +S G R+ LIP+SAHGTNP
Sbjct: 546 SNLSEDLKVITGFAGVSLQPNSGAAGEYAGLRVIRAYLESIGQGHRNKILIPASAHGTNP 605
Query: 602 ATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIREICG 661
A+A AG V ACD +GNVD+ DLRAKA E+++ LAALMITYPSTHG+FE I+EIC
Sbjct: 606 ASAIQAGFETVTCACDEQGNVDMGDLRAKAEENKEALAALMITYPSTHGIFETEIKEICE 665
Query: 662 IIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSH 721
IIH G QVY+DGANMNA VGL PG G DV HLNLHKTF PHGGGGPGVGPI V H
Sbjct: 666 IIHACGAQVYMDGANMNAQVGLTNPGFIGADVCHLNLHKTFASPHGGGGPGVGPICVAEH 725
Query: 722 LTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYISMMGGAGLKRASQLAILNANYISR 781
L PFLPGH+ + V AAPFGSA ILPIT+ YI MMG GL +A+++AILNANY++
Sbjct: 726 LVPFLPGHSIFGSTQNQVSAAPFGSAGILPITYGYIRMMGTEGLTQATKIAILNANYLAA 785
Query: 782 RLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGT 841
L++ Y ++Y G+ G V HE IL+ R + + +GIS +D+AKRL+D+G+HAPT+SFPV GT
Sbjct: 786 CLKDTYGIVYRGATGFVGHEMILECRKVHEETGISENDIAKRLMDYGYHAPTLSFPVHGT 845
Query: 842 LMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTAAELVSE-WTH 900
LMIEPTESES ELD F + M+ I +EI+ V+N DK+DN L NAPH E+V++ W H
Sbjct: 846 LMIEPTESESLAELDNFVDVMLNIWKEIQEVKNEEADKNDNVLINAPHPEYEIVNDNWEH 905
Query: 901 PYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLV 936
YTRE+A YP+ S+ E K+W V RVDN GDR L+
Sbjct: 906 SYTREKAAYPIESVRENKFWVNVARVDNTLGDRKLL 941
Lambda K H
0.319 0.135 0.398
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1951
Number of extensions: 68
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 946
Length of database: 949
Length adjustment: 44
Effective length of query: 902
Effective length of database: 905
Effective search space: 816310
Effective search space used: 816310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)
Align candidate 350675 BT1147 (glycine dehydrogenase [decarboxylating] (NCBI ptt file))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR00461.hmm
# target sequence database: /tmp/gapView.18531.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00461 [M=939]
Accession: TIGR00461
Description: gcvP: glycine dehydrogenase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1296.4 0.1 0 1296.2 0.1 1.0 1 lcl|FitnessBrowser__Btheta:350675 BT1147 glycine dehydrogenase [de
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350675 BT1147 glycine dehydrogenase [decarboxylating] (NCBI ptt file)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1296.2 0.1 0 0 1 936 [. 9 941 .. 9 944 .. 0.97
Alignments for each domain:
== domain 1 score: 1296.2 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyat 76
rh+G +e + ml+ +G+d+l++li++ +p +irl+ pl l p +eye +++ +asknk +++yiG G+y+t
lcl|FitnessBrowser__Btheta:350675 9 RHIGINEEDTAVMLRKIGVDSLDELINKTIPANIRLKEPLALAKPLTEYEFGKHIADLASKNKLYTTYIGLGWYNT 84
9*************************************************************************** PP
TIGR00461 77 ilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrv...s 149
i+p viqrn++enp wyt+ytpyq+e+sqGrleal+nfqt v dlt +++an sllde+taaaea+ + + + +
lcl|FitnessBrowser__Btheta:350675 85 ITPAVIQRNVFENPVWYTSYTPYQTEVSQGRLEALMNFQTAVCDLTAMPLANCSLLDEATAAAEAVTMMYALrsrT 160
*****************************************************************99999874222 PP
TIGR00461 150 kkk..ankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrk 223
++k an +v++++ pqtl v+ tra p gie+ v+ ++++ + +++ ++lqyp ++G++ dy ++++++++
lcl|FitnessBrowser__Btheta:350675 161 QQKagANVVFVDENIFPQTLAVMTTRAIPQGIELRVGKYKEFEPSPEIFACILQYPNSSGNVEDYADFTKKAHEAD 236
344468999******************************************************************* PP
TIGR00461 224 alvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrl 299
v+vaad+l+l+lltppg+ Gadiv+G++qr+G p+ yGGp a +fa++deykr++pGri+G skd+ G+ r+
lcl|FitnessBrowser__Btheta:350675 237 CKVAVAADILSLALLTPPGEWGADIVFGTTQRLGTPMFYGGPSAGYFATRDEYKRNMPGRIIGWSKDKYGKLCYRM 312
**************************************************************************** PP
TIGR00461 300 alqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtlt 375
alqtreqhi+r+katsnictaq+lla++a yavyhG G+k ia ri+++t+ l + lk+ +y n++yfdtl+
lcl|FitnessBrowser__Btheta:350675 313 ALQTREQHIKREKATSNICTAQALLATMAGFYAVYHGQEGIKTIASRIHSITVFLDKQLKKFGYTQVNAQYFDTLR 388
**************************************************************************** PP
TIGR00461 376 vevgekaase.vlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedv.ansfpae 449
e+ e+++++ + + a ++e+nlr ++vg+++dett + ll ++a+ g + +++++ ++ ++++
lcl|FitnessBrowser__Btheta:350675 389 FELPEHVSAQqIRTIALSKEVNLRYYENGDVGFSIDETTDIAATNVLLSIFAIAA--GKDYQKVEDVPeKSNIDKA 462
*****9988779999**************************************66..6666666543314479*** PP
TIGR00461 450 llrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqv 525
l+r+ +l++evf +yh+ete++ry++rl++kd++l+qsmi lGsctmklna+aemlp++ pef +hp+ p +q+
lcl|FitnessBrowser__Btheta:350675 463 LKRTTPFLTHEVFSNYHTETEMMRYIKRLDRKDISLAQSMISLGSCTMKLNAAAEMLPLSRPEFMSMHPLVPEDQA 538
**************************************************************************** PP
TIGR00461 526 eGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlk 601
eGy+eli++l ++l itGf ++slqpnsGa GeyaGlrvir y+es g++hrn lipasahGtnpasa aG++
lcl|FitnessBrowser__Btheta:350675 539 EGYRELISNLSEDLKVITGFAGVSLQPNSGAAGEYAGLRVIRAYLESIGQGHRNKILIPASAHGTNPASAIQAGFE 614
**************************************************************************** PP
TIGR00461 602 vvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltsp 677
v+ +cd++Gn+d+ dl+akae++ + laa+m+typst+G+fe+ i+e+++i+h G qvy+dGanmnaqvGlt+p
lcl|FitnessBrowser__Btheta:350675 615 TVTCACDEQGNVDMGDLRAKAEENKEALAALMITYPSTHGIFETEIKEICEIIHACGAQVYMDGANMNAQVGLTNP 690
**************************************************************************** PP
TIGR00461 678 gdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisy 753
g++Gadvchlnlhktf+ phGGGGpg+gpi+v hl+pflp++++ ++++vsaap+Gsa ilpi+y
lcl|FitnessBrowser__Btheta:350675 691 GFIGADVCHLNLHKTFASPHGGGGPGVGPICVAEHLVPFLPGHSIFG--------STQNQVSAAPFGSAGILPITY 758
******************************************76643........34678**************** PP
TIGR00461 754 myikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfh 829
yi+mmG+eGl++a+++ailnanyla+ lkd+y i+++g + v he+il+ r++ e++gi++ d+akrl+dyG+h
lcl|FitnessBrowser__Btheta:350675 759 GYIRMMGTEGLTQATKIAILNANYLAACLKDTYGIVYRGATGFVGHEMILECRKVHEETGISENDIAKRLMDYGYH 834
**************************************************************************** PP
TIGR00461 830 aptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysre 905
aptlsfpv Gtlm+eptesesl eld f+d m+ i +ei++vk+ e +++dn+l naph + + +w ++y+re
lcl|FitnessBrowser__Btheta:350675 835 APTLSFPVHGTLMIEPTESESLAELDNFVDVMLNIWKEIQEVKNEEADKNDNVLINAPHPEYEIVNDNWEHSYTRE 910
***********************************************************8888888889999**** PP
TIGR00461 906 eaaypapvlkyfkfwptvarlddtyGdrnlv 936
+aayp+ ++++kfw var+d+t Gdr+l+
lcl|FitnessBrowser__Btheta:350675 911 KAAYPIESVRENKFWVNVARVDNTLGDRKLL 941
*****************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (949 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 12.64
//
[ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory