Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate WP_019556676.1 F612_RS0105105 aminomethyl-transferring glycine dehydrogenase
Query= reanno::WCS417:GFF4367
(946 letters)
>NCBI__GCF_000381085.1:WP_019556676.1
Length = 973
Score = 1209 bits (3129), Expect = 0.0
Identities = 602/954 (63%), Positives = 732/954 (76%), Gaps = 13/954 (1%)
Query: 4 QLTTANEFIARHIGPRQEDEQQMLASLGFDSLEALSASVIPESIKGTSVLGLEDGLSEAE 63
+L +++FI RH+GP +++ ML SL SL L V+P SI+ + L +GL+E +
Sbjct: 16 ELQQSDKFITRHLGPDDDEQLAMLRSLKMASLNELLDKVVPSSIRRHDPMDLAEGLTEQQ 75
Query: 64 ALAKIKAIAGKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEA 123
+L K+KAIA KN + K+YIG GYYN TP I RN+LENPAWYTAYTPYQ EISQGRLEA
Sbjct: 76 SLEKLKAIASKNIVLKSYIGMGYYNTFTPPTIQRNILENPAWYTAYTPYQAEISQGRLEA 135
Query: 124 LLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASIHSHPQTLDV 183
+LNFQT++SDLTGL +ANASLLDEATA AEAMT C+R+SK+KG FF + HPQ ++V
Sbjct: 136 MLNFQTMVSDLTGLELANASLLDEATACAEAMTLCQRMSKSKGK-VFFVADDCHPQNIEV 194
Query: 184 LRTRAEPLGIDVVVGDE-RELTDVSPFFGALLQYPASNGDVFDYRELTERFHAAHGLVAV 242
++TRAEPLGI+VVVG+ EL D FG LLQYP + G+V D+ EL E+ HA LVA+
Sbjct: 195 IQTRAEPLGIEVVVGNPINELADYD-LFGVLLQYPGTYGEVSDFSELIEKIHAKKALVAM 253
Query: 243 AADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVS 302
+ADLLALTLL PGE GADVAIG+ QRFGVPLG+GGPHAAY +TKD FKR MPGRL+GVS
Sbjct: 254 SADLLALTLLKTPGEMGADVAIGNTQRFGVPLGYGGPHAAYMATKDDFKRSMPGRLIGVS 313
Query: 303 VDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIARRVH 362
VD GK A RLA+QTREQHIRREKATSNICTAQ LLA +ASMYAVYHGP GLT+IA RVH
Sbjct: 314 VDSRGKKAYRLALQTREQHIRREKATSNICTAQALLAVMASMYAVYHGPVGLTKIAYRVH 373
Query: 363 QLTAILAKGLTALGQNVEQAHFFDTLTLNTGANTAAVHDKARAQRINLRVVDAERVGVSV 422
+ T + A GLT LG V +FDTL + A+ A + INLR +DA+ VG+S
Sbjct: 374 RYTQLFANGLTQLGFKVNNKVYFDTLNIFVPGKAVAIQQAAVDKGINLRPIDADTVGLSF 433
Query: 423 DETTTQADIETLWAIFADGKALPDFAAQVESTLPAA----LLRQSPVLSHPVFNRYHSET 478
DE++T DI LW +FA +A+ A + P LLR S L+HPVF+ + SET
Sbjct: 434 DESSTLQDITVLWEVFAGEQAVSLKAEVLMKDQPPVIGEDLLRTSEFLTHPVFHEHRSET 493
Query: 479 ELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYL 538
++MRY+R LADKDLALDR MIPLGSCTMKLNAA+E++P++W EF LHPF P Q+ GY
Sbjct: 494 QMMRYMRCLADKDLALDRAMIPLGSCTMKLNAAAELMPISWPEFANLHPFVPLNQALGYQ 553
Query: 539 ELTSDLEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGDERRDICLIPSSAHG 598
++ +LE MLC ATGYDA+SLQPN+G+QGEYAGLLAIRAYH+SRG+ RD+CLIP+SAHG
Sbjct: 554 QMVLELEKMLCEATGYDAVSLQPNSGAQGEYAGLLAIRAYHKSRGEGHRDVCLIPASAHG 613
Query: 599 TNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHRDHLAALMITYPSTHGVFEEGIRE 658
TNPA+A M GM VVV + +G +D+ DL AK +H LAA+MITYPSTHGVFEE ++
Sbjct: 614 TNPASAQMVGMSVVVVKTNLKGEIDLADLHAKLEKHSAKLAAIMITYPSTHGVFEENVKT 673
Query: 659 ICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGV 718
+C ++H +GGQVYIDGANMNAMVG+ APG+FGGDVSHLNLHKTF IPHGGGGPGVGPIGV
Sbjct: 674 VCDLVHQHGGQVYIDGANMNAMVGVAAPGQFGGDVSHLNLHKTFAIPHGGGGPGVGPIGV 733
Query: 719 KSHLTPFLPGHAAMERKE-----GAVCAAPFGSASILPITWMYISMMGGAGLKRASQLAI 773
HL PFLPG+A + ++ GAV AAP+GSA +LPI+W YI+MMG GL +A+ AI
Sbjct: 734 GKHLKPFLPGYAVVNSEDEPKVVGAVSAAPWGSAGVLPISWSYIAMMGSNGLVQATATAI 793
Query: 774 LNANYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPT 833
LNANYI+ L HYP+LY+ G VAHECI+DLRP+K++SGI+VDD+AKRLID+GFHAPT
Sbjct: 794 LNANYIAHSLAPHYPILYSDDQGRVAHECIIDLRPIKEASGITVDDIAKRLIDYGFHAPT 853
Query: 834 MSFPVAGTLMIEPTESESKEELDRFCNAMIAIREEIRAVENGTLDKDDNPLKNAPHTA-A 892
MSFPVAGT MIEPTESESK ELDRFC+AMIAI+ EI V +G LD+ DNPLKNAPHTA
Sbjct: 854 MSFPVAGTFMIEPTESESKVELDRFCDAMIAIKAEINDVMSGVLDEHDNPLKNAPHTADM 913
Query: 893 ELVSEWTHPYTREQAVYPVPSLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 946
+ EW H Y+R+ A YPV SL E KYW PVGRVDNV+GDR+LVC+CP + Y+
Sbjct: 914 VMADEWNHAYSRQLAAYPVESLREVKYWCPVGRVDNVYGDRHLVCSCPPLSDYS 967
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: 2071
Number of extensions: 69
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: 973
Length adjustment: 44
Effective length of query: 902
Effective length of database: 929
Effective search space: 837958
Effective search space used: 837958
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 WP_019556676.1 F612_RS0105105 (aminomethyl-transferring glycine dehydrogenase)
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.843220.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 1496.7 0.2 0 1496.6 0.2 1.0 1 NCBI__GCF_000381085.1:WP_019556676.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381085.1:WP_019556676.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1496.6 0.2 0 0 1 939 [] 26 960 .. 26 960 .. 1.00
Alignments for each domain:
== domain 1 score: 1496.6 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGy 73
rhlGpd+ eq ml++l + +ln+l++++vp +ir + p+ l +e++ l++lk+iaskn ++ksyiG+Gy
NCBI__GCF_000381085.1:WP_019556676.1 26 RHLGPDDDEQLAMLRSLKMASLNELLDKVVPSSIRRHDPMDLAEGLTEQQSLEKLKAIASKNIVLKSYIGMGY 98
9************************************************************************ PP
TIGR00461 74 yatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsf 146
y+t +pp iqrn+lenp wytaytpyq+eisqGrlea+lnfqt+v+dltGle+anasllde+ta aeam l++
NCBI__GCF_000381085.1:WP_019556676.1 99 YNTFTPPTIQRNILENPAWYTAYTPYQAEISQGRLEAMLNFQTMVSDLTGLELANASLLDEATACAEAMTLCQ 171
************************************************************************* PP
TIGR00461 147 rvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidel 219
r+sk+k + f+va+d+hpq +ev++traeplgiev+v++ + d++Gvllqyp+t Ge+ d+ +li+++
NCBI__GCF_000381085.1:WP_019556676.1 172 RMSKSKGKVFFVADDCHPQNIEVIQTRAEPLGIEVVVGNPINELADYDLFGVLLQYPGTYGEVSDFSELIEKI 244
*****************************************999***************************** PP
TIGR00461 220 ksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdal 292
+ +kalv+++adllaltll++pg++Gad+++G +qrfGvplGyGGphaa++a+kd++kr++pGr++Gvs d+
NCBI__GCF_000381085.1:WP_019556676.1 245 HAKKALVAMSADLLALTLLKTPGEMGADVAIGNTQRFGVPLGYGGPHAAYMATKDDFKRSMPGRLIGVSVDSR 317
************************************************************************* PP
TIGR00461 293 GntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyel 365
G+ a rlalqtreqhirr+katsnictaq+lla++as+yavyhGp+Gl +ia r++r t+++a+gl + ++++
NCBI__GCF_000381085.1:WP_019556676.1 318 GKKAYRLALQTREQHIRREKATSNICTAQALLAVMASMYAVYHGPVGLTKIAYRVHRYTQLFANGLTQLGFKV 390
************************************************************************* PP
TIGR00461 366 rnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseel 438
+nk yfdtl + v ka ++++aa +++inlr++++++vg+++de+ t +d++ l++v+ag++ +l++e l
NCBI__GCF_000381085.1:WP_019556676.1 391 NNKVYFDTLNIFVPGKAV-AIQQAAVDKGINLRPIDADTVGLSFDESSTLQDITVLWEVFAGEQAVSLKAEVL 462
*************98887.9***************************************************** PP
TIGR00461 439 sedvansfpaellrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwp 511
+d + ++llr++e+l+++vf+++ set+++ry+ l kdlal+++miplGsctmklna+ae++pi+wp
NCBI__GCF_000381085.1:WP_019556676.1 463 MKDQPPVIGEDLLRTSEFLTHPVFHEHRSETQMMRYMRCLADKDLALDRAMIPLGSCTMKLNAAAELMPISWP 535
************************************************************************* PP
TIGR00461 512 efaeihpfapaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclip 584
efa++hpf p +q+ Gy++++ +lek l+e tG+da+slqpnsGaqGeyaGl +ir yh+srge+hr++clip
NCBI__GCF_000381085.1:WP_019556676.1 536 EFANLHPFVPLNQALGYQQMVLELEKMLCEATGYDAVSLQPNSGAQGEYAGLLAIRAYHKSRGEGHRDVCLIP 608
************************************************************************* PP
TIGR00461 585 asahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrf 657
asahGtnpasa+m+G+ vv+vk + +G+idl dl+ak ek++ +laa+m+typst+Gvfee +++v+d+vh+
NCBI__GCF_000381085.1:WP_019556676.1 609 ASAHGTNPASAQMVGMSVVVVKTNLKGEIDLADLHAKLEKHSAKLAAIMITYPSTHGVFEENVKTVCDLVHQH 681
************************************************************************* PP
TIGR00461 658 GGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvveleg 730
GGqvy+dGanmna vG+++pg++G dv+hlnlhktf+iphGGGGpg+gpigv hl+pflp+ vv+ e
NCBI__GCF_000381085.1:WP_019556676.1 682 GGQVYIDGANMNAMVGVAAPGQFGGDVSHLNLHKTFAIPHGGGGPGVGPIGVGKHLKPFLPG---YAVVNSED 751
**************************************************************...889999** PP
TIGR00461 731 esksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecil 803
e k +gavsaap+Gsa +lpis+ yi+mmG++Gl +a+ ailnany+a+ l +y+il+ ++rvaheci+
NCBI__GCF_000381085.1:WP_019556676.1 752 EPKVVGAVSAAPWGSAGVLPISWSYIAMMGSNGLVQATATAILNANYIAHSLAPHYPILYSDDQGRVAHECII 824
************************************************************************* PP
TIGR00461 804 dlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGei 876
dlr++ke +gi + d+akrl+dyGfhapt+sfpvaGt+m+epteses++eldrf+damiaik+ei+ v++G++
NCBI__GCF_000381085.1:WP_019556676.1 825 DLRPIKEASGITVDDIAKRLIDYGFHAPTMSFPVAGTFMIEPTESESKVELDRFCDAMIAIKAEINDVMSGVL 897
************************************************************************* PP
TIGR00461 877 klednilknaphslqslivaewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
+ +dn+lknaph+++ +++ ew+++ysr+ aayp+ l++ k+w v+r+d++yGdr+lvcsc
NCBI__GCF_000381085.1:WP_019556676.1 898 DEHDNPLKNAPHTADMVMADEWNHAYSRQLAAYPVESLREVKYWCPVGRVDNVYGDRHLVCSC 960
*************************************************************** PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (973 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 43.18
//
[ok]
This GapMind analysis is from Apr 09 2024. 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