Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate Ac3H11_167 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
Query= reanno::WCS417:GFF4367
(946 letters)
>FitnessBrowser__acidovorax_3H11:Ac3H11_167
Length = 970
Score = 1201 bits (3107), Expect = 0.0
Identities = 602/958 (62%), Positives = 731/958 (76%), Gaps = 17/958 (1%)
Query: 5 LTTANEFIARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLSEAEA 64
L A EF+ RHIG DE ML+ +G S L S++P SI + + L +EA A
Sbjct: 14 LENAAEFLPRHIGIDAADEAHMLSVIGEASRRTLIDSIVPRSIARSRAMDLPAATTEAAA 73
Query: 65 LAKIKAIAGKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEAL 124
LA++KAIAGKN++ K++IGQGYY HTP ILRN+LENPAWYTAYTPYQ EISQGR+EAL
Sbjct: 74 LAELKAIAGKNKVLKSFIGQGYYGTHTPGVILRNILENPAWYTAYTPYQAEISQGRMEAL 133
Query: 125 LNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASIHSHPQTLDVL 184
+NFQT++ DLTG+PIANAS+LDEATAAAEAMT KR K+K SN F + +HPQT++V+
Sbjct: 134 VNFQTMVCDLTGMPIANASMLDEATAAAEAMTLAKRSVKSK-SNVFVVAGDAHPQTIEVI 192
Query: 185 RTRAEPLGIDVVVGDERELTD---VSPFFGALLQYPASNGDVFDYRELTERFHAAHGLVA 241
+TRA+PLG+DV + + E D +F L QYPA++G + D R E+ HA
Sbjct: 193 QTRAKPLGLDVRLANSAEEWDSLLAGDYFAVLAQYPATSGRIDDLRADVEKAHAKQAAFI 252
Query: 242 VAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGV 301
VAADLLALTL+TPPGE GAD+ +G+ QRFG+P+G GGPHAA+ + +D FKR +PGRLVGV
Sbjct: 253 VAADLLALTLITPPGEQGADIVVGTTQRFGMPMGAGGPHAAFMACRDEFKRSLPGRLVGV 312
Query: 302 SVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARRV 361
SVD GKPA RLA+QTREQHIRREKATSNICTAQVL A +ASMYAVYHGP+GL++IA+RV
Sbjct: 313 SVDVHGKPAYRLALQTREQHIRREKATSNICTAQVLPAVVASMYAVYHGPEGLSRIAQRV 372
Query: 362 HQLTAILAKGLTALGQNVEQAHFFDTLTLNTGANTAAVHDKARAQRINLRVVDAERVGVS 421
TAILA+GL LG V + FDTL L T T ++ KA NLR+ + +S
Sbjct: 373 ASYTAILARGLVQLGAPVREQATFDTLVLKTDGATKSIATKAIQSGANLRIYFESYLCIS 432
Query: 422 VDETTTQADIETLWAIFA-DGKALPDFAA---QVESTLPAALLRQSPVLSHPVFNRYHSE 477
+DETTT+ADIE LW +FA DG+ALP F A VE +PAAL R S L+HPVFN +HSE
Sbjct: 433 LDETTTRADIELLWKVFAKDGQALPTFDAFENGVEPLIPAALRRTSRYLTHPVFNTHHSE 492
Query: 478 TELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGY 537
T ++RY+R+L+DKDLALDR+MIPLGSCTMKLNA SEMIP+TW EF +HPFAPA+Q GY
Sbjct: 493 TGMLRYIRQLSDKDLALDRSMIPLGSCTMKLNATSEMIPITWPEFANMHPFAPADQQQGY 552
Query: 538 LELTSDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAH 597
L L A LC ATGY ISLQPNAGSQGEYAGLLAI+ YH+SRG+ R+ICLIPSSAH
Sbjct: 553 KALDEQLRAWLCEATGYAGISLQPNAGSQGEYAGLLAIKGYHESRGEGHRNICLIPSSAH 612
Query: 598 GTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIR 657
GTNPA+A M GM+VVVTACDA GNVD+ DL+AK +H ++A +MITYPSTHGVFE ++
Sbjct: 613 GTNPASAQMVGMQVVVTACDANGNVDLADLQAKCEQHSGNIACVMITYPSTHGVFETSVK 672
Query: 658 EICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIG 717
E+C ++H +GG+VY+DGANMNA+VG+ APG+FGGDVSHLNLHKTFCIPHGGGGPGVGP+
Sbjct: 673 ELCALVHSHGGRVYVDGANMNALVGVAAPGEFGGDVSHLNLHKTFCIPHGGGGPGVGPVC 732
Query: 718 VKSHLTPFLPG--------HAAMERKEGAVCAAPFGSASILPITWMYISMMGGAGLKRAS 769
V L PFLPG + K G V AAP G+A++LPI+WMYI MMG GL+ A+
Sbjct: 733 VVEDLVPFLPGLPGQGDQPKSPATGKVGPVSAAPLGNAAVLPISWMYIRMMGADGLQAAT 792
Query: 770 QLAILNANYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGF 829
+ AIL+ANYIS RL++HYP LY NG VAHECILDLR LKD+SG+ +DVAKRLID+GF
Sbjct: 793 ETAILSANYISARLKDHYPTLYASENGHVAHECILDLRGLKDTSGVMAEDVAKRLIDYGF 852
Query: 830 HAPTMSFPVAGTLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPH 889
HAPT+SFPV TLM+EPTESE+ E+DRF +AMIAIREEIR +E G L +D+NPLKNAPH
Sbjct: 853 HAPTLSFPVPNTLMVEPTESETLFEIDRFIDAMIAIREEIRQIEAGKLPQDNNPLKNAPH 912
Query: 890 TAAELVS-EWTHPYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 946
TA L+S EWT PYTRE A YPV +L + KYW PVGRVDNV+GDRNL C+C + YA
Sbjct: 913 TAENLLSGEWTRPYTREAAAYPVAALRQAKYWSPVGRVDNVWGDRNLSCSCIPVSDYA 970
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: 2197
Number of extensions: 87
Number of successful extensions: 8
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: 970
Length adjustment: 44
Effective length of query: 902
Effective length of database: 926
Effective search space: 835252
Effective search space used: 835252
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 Ac3H11_167 (Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2))
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.15222.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 1430.7 0.0 0 1430.5 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 Glycine dehydrogenase [decarboxy
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P pr
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1430.5 0.0 0 0 1 939 [] 23 963 .. 23 963 .. 0.98
Alignments for each domain:
== domain 1 score: 1430.5 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknk 63
rh+G d+a+ +ml +G + li+ +vp++i +r++ l+a+++e +alaelk+ia knk
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 23 RHIGIDAADEAHMLSVIGEASRRTLIDSIVPRSIARSRAMDLPAATTEAAALAELKAIAGKNK 85
9************************************************************** PP
TIGR00461 64 kvksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlev 126
++ks+iG+Gyy+t +p vi+rn+lenp wytaytpyq+eisqGr+eal+nfqt+v dltG+++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 86 VLKSFIGQGYYGTHTPGVILRNILENPAWYTAYTPYQAEISQGRMEALVNFQTMVCDLTGMPI 148
*************************************************************** PP
TIGR00461 127 anaslldegtaaaeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddas.. 187
anas+lde+taaaeam l++r k+k+n fvva d hpqt+ev++tra+plg++v ++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 149 ANASMLDEATAAAEAMTLAKRSVKSKSNVFVVAGDAHPQTIEVIQTRAKPLGLDVRLANSAee 211
*******************************************************87665411 PP
TIGR00461 188 .kvkkavdvlGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadiv 249
+ a d + vl qypat+G i d++a +++++ ++a vaadllaltl+tppg++Gadiv
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 212 wDSLLAGDYFAVLAQYPATSGRIDDLRADVEKAHAKQAAFIVAADLLALTLITPPGEQGADIV 274
14556789******************************************************* PP
TIGR00461 250 lGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdk 312
+G++qrfG+p+G GGphaaf+a++de+kr+lpGr+vGvs d +G++a rlalqtreqhirr+k
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 275 VGTTQRFGMPMGAGGPHAAFMACRDEFKRSLPGRLVGVSVDVHGKPAYRLALQTREQHIRREK 337
*************************************************************** PP
TIGR00461 313 atsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtlt 375
atsnictaqvl a+vas+yavyhGp Gl +ia+r+ + t+ila gl + + +r++ fdtl
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 338 ATSNICTAQVLPAVVASMYAVYHGPEGLSRIAQRVASYTAILARGLVQLGAPVREQATFDTLV 400
**************************************************************9 PP
TIGR00461 376 vevgekaasevlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseel 438
++ ++a+ ++ ++a + + nlr + + i+ldettt++d++ l+kv+a + + + + +
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 401 LKT-DGATKSIATKAIQSGANLRIYFESYLCISLDETTTRADIELLWKVFAKDGQALPTFDAF 462
985.777779999999***********************************9666666899** PP
TIGR00461 439 sedvansfpaellrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklna 501
++ v+ +pa+l+r++ +l+++vfn++hset +lry+ +l kdlal++smiplGsctmklna
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 463 ENGVEPLIPAALRRTSRYLTHPVFNTHHSETGMLRYIRQLSDKDLALDRSMIPLGSCTMKLNA 525
*************************************************************** PP
TIGR00461 502 taemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlr 564
t em+pitwpefa++hpfapa+q +Gyk l ql +wl+e tG+ +islqpn+G+qGeyaGl
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 526 TSEMIPITWPEFANMHPFAPADQQQGYKALDEQLRAWLCEATGYAGISLQPNAGSQGEYAGLL 588
*************************************************************** PP
TIGR00461 565 virsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagd 627
+i+ yhesrge+hrniclip sahGtnpasa+m+G++vv+ +cd +Gn+dl dl+ak e+++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 589 AIKGYHESRGEGHRNICLIPSSAHGTNPASAQMVGMQVVVTACDANGNVDLADLQAKCEQHSG 651
*************************************************************** PP
TIGR00461 628 elaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlh 690
++a+vm+typst+Gvfe++++e++ +vh+ GG+vy+dGanmna vG+++pg++G dv+hlnlh
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 652 NIACVMITYPSTHGVFETSVKELCALVHSHGGRVYVDGANMNALVGVAAPGEFGGDVSHLNLH 714
*************************************************************** PP
TIGR00461 691 ktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisy 753
ktf+iphGGGGpg+gp++v l+pflp+ + + ++g vsaap G+a++lpis+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 715 KTFCIPHGGGGPGVGPVCVVEDLVPFLPGLPGQGDQPKSPATGKVGPVSAAPLGNAAVLPISW 777
*****************************888888888888999******************* PP
TIGR00461 754 myikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiea 816
myi+mmGa+Gl+ a+e ail+any+ +rlkd+y+ l+ +++++vahecildlr lk+ +g+ a
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 778 MYIRMMGADGLQAATETAILSANYISARLKDHYPTLYASENGHVAHECILDLRGLKDTSGVMA 840
*************************************************************** PP
TIGR00461 817 ldvakrlldyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeikle 879
+dvakrl+dyGfhaptlsfpv+ tlmveptese+l e+drfidamiai+eei ++ aG+++++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 841 EDVAKRLIDYGFHAPTLSFPVPNTLMVEPTESETLFEIDRFIDAMIAIREEIRQIEAGKLPQD 903
*************************************************************** PP
TIGR00461 880 dnilknaphslqslivaewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
+n+lknaph++++l+ +ew+ py+re aayp++ l++ k+w v+r+d+++Gdrnl csc
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_167 904 NNPLKNAPHTAENLLSGEWTRPYTREAAAYPVAALRQAKYWSPVGRVDNVWGDRNLSCSC 963
************************************************************ PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (970 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.07
# Mc/sec: 12.30
//
[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:
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