Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate WP_090443896.1 BLS63_RS11160 glycine dehydrogenase (aminomethyl-transferring)
Query= CharProtDB::CH_003480
(957 letters)
>NCBI__GCF_900100495.1:WP_090443896.1
Length = 958
Score = 1256 bits (3251), Expect = 0.0
Identities = 623/960 (64%), Positives = 759/960 (79%), Gaps = 8/960 (0%)
Query: 1 MTQTLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGA 60
+T +LSQL+ AF+ RH+GPDAA+QQ ML A+G S AL Q VP I+L P ++
Sbjct: 3 VTPSLSQLQQPDAFLRRHLGPDAAEQQAMLAALGVPSRAALIEQTVPPAIRLNRPLELPP 62
Query: 61 PATEYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVS 120
E ALA+L+ A +N+ +TS IGMGY P VILRN+LENPGWYTAYTPYQPE++
Sbjct: 63 ALDEQGALAKLRGYAEQNQLWTSLIGMGYHGTLTPTVILRNVLENPGWYTAYTPYQPEIA 122
Query: 121 QGRLEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVH 180
QGRLEALLNFQQ+ +DLTGL++A+ASLLDEATAAAEAMA+AKRV+K K+ N FFV + H
Sbjct: 123 QGRLEALLNFQQLCIDLTGLELANASLLDEATAAAEAMALAKRVAKSKS-NLFFVDENCH 181
Query: 181 PQTLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRK 240
PQTL VV+TRA FGFE++VD + HQ VFG LLQ + GEI D LI++L +++
Sbjct: 182 PQTLSVVQTRAAAFGFELVVDAVANLGQHQ-VFGALLQYPDSHGEIRDLRPLIAQLHAQQ 240
Query: 241 IVVSVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGR 300
+ VA D+++L+LLT PG+ GAD+ FGSAQRFGVPMGYGGPHAAFFA +DE+KR+MPGR
Sbjct: 241 ALACVACDLLSLLLLTPPGELGADVAFGSAQRFGVPMGYGGPHAAFFATRDEFKRAMPGR 300
Query: 301 IIGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRI 360
IIGVSKDA GN ALRMA+QTREQHIRREKANSNICT+QVLLANIA YAVYHGP GLKRI
Sbjct: 301 IIGVSKDARGNVALRMALQTREQHIRREKANSNICTAQVLLANIAGFYAVYHGPEGLKRI 360
Query: 361 ANRIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVA-DKAGVLTRAEAAEINLRSDILNA 419
A R+HRLT +LAAGL Q G+ + H+FDTL +EV + ++ A+AA INLR
Sbjct: 361 AQRVHRLTALLAAGLAQNGIARDNRHFFDTLTLEVGGSQTAIIESAQAARINLRILGRGK 420
Query: 420 VGITLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVF 479
+G++LDET +M+LF + LG +HGL + LD+ I + R L HPVF
Sbjct: 421 LGVSLDETCDEHTLMRLFAIFLGADHGLSVTKLDE--GEIGGGIPSELARSSAYLRHPVF 478
Query: 480 NRYHSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPP 539
N +HSETEM+RY+ LE KDLALNQAMIPLGSCTMKLNA++EMIPITWP+FA+LHPF P
Sbjct: 479 NSHHSETEMLRYLKQLENKDLALNQAMIPLGSCTMKLNASSEMIPITWPQFADLHPFVPV 538
Query: 540 EQAEGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICL 599
EQA+GY+ +I +L WL +TG+DA+CMQPNSGAQGEYAGLLAIR YH+SR + R++CL
Sbjct: 539 EQAQGYRLLIDELEAWLRAITGFDAICMQPNSGAQGEYAGLLAIRKYHDSRGDSQRNVCL 598
Query: 600 IPASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGV 659
IPASAHGTNPASA MA +++V+V CD +GN+DL DL+ KA +AG+ L+C+M+TYPSTHGV
Sbjct: 599 IPASAHGTNPASAQMASLRIVIVECDSHGNVDLDDLKRKALEAGEQLACLMITYPSTHGV 658
Query: 660 YEETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGP 719
YEE IRE+CEVVH GGQVY+DGAN+NAQVG+T P IGADVSH+NLHKTFCIPHGGGGP
Sbjct: 659 YEEGIREICEVVHAQGGQVYMDGANLNAQVGLTRPADIGADVSHMNLHKTFCIPHGGGGP 718
Query: 720 GMGPIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLK 779
GMGPIGVKAHLAPFV H V++++G + GAVS AP+GSASILPISWMYI MMG + L
Sbjct: 719 GMGPIGVKAHLAPFVANHPVIELQGPDPQNGAVSGAPWGSASILPISWMYIAMMGPQ-LA 777
Query: 780 KASQVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLID 839
AS+VAIL+ANY+A +L AFP+LY+GR+GRVAHECILD+RPLK +TGISE D+AKRL+D
Sbjct: 778 DASEVAILSANYLAQQLGGAFPLLYSGRNGRVAHECILDLRPLKAQTGISEEDVAKRLMD 837
Query: 840 YGFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVN 899
YGFHAPTMSFPV GTLM+EPTESESK ELDRFI+AML+IRAEI +V +G WP EDNPL
Sbjct: 838 YGFHAPTMSFPVPGTLMIEPTESESKHELDRFIEAMLSIRAEIAKVHSGDWPAEDNPLKR 897
Query: 900 APHIQSELVAEWAHPYSREVAVFPA--GVADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
APH ++++ W PYS E AV P A KYWPTV R+D+VYGDRNLFC+CVP+ EY+
Sbjct: 898 APHTLADVIGVWERPYSLEQAVTPTAHSRAHKYWPTVNRVDNVYGDRNLFCACVPLDEYR 957
Lambda K H
0.319 0.134 0.395
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: 2263
Number of extensions: 70
Number of successful extensions: 7
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: 957
Length of database: 958
Length adjustment: 44
Effective length of query: 913
Effective length of database: 914
Effective search space: 834482
Effective search space used: 834482
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_090443896.1 BLS63_RS11160 (glycine dehydrogenase (aminomethyl-transferring))
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.15551.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 1527.1 0.0 0 1526.9 0.0 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090443896.1 BLS63_RS11160 glycine dehydrogen
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090443896.1 BLS63_RS11160 glycine dehydrogenase (aminomethyl-transferring)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1526.9 0.0 0 0 1 939 [] 19 950 .. 19 950 .. 0.99
Alignments for each domain:
== domain 1 score: 1526.9 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyi 69
rhlGpd+aeq+ ml +lG+ + alieq vp++irl+rpl+l+ + e++ala+l+ a++n+ +s i
lcl|NCBI__GCF_900100495.1:WP_090443896.1 19 RHLGPDAAEQQAMLAALGVPSRAALIEQTVPPAIRLNRPLELPPALDEQGALAKLRGYAEQNQLWTSLI 87
9******************************************************************** PP
TIGR00461 70 GkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaa 138
G+Gy +t++p vi+rn+lenpgwytaytpyqpei+qGrleallnfq++ +dltGle+anasllde+taa
lcl|NCBI__GCF_900100495.1:WP_090443896.1 88 GMGYHGTLTPTVILRNVLENPGWYTAYTPYQPEIAQGRLEALLNFQQLCIDLTGLELANASLLDEATAA 156
********************************************************************* PP
TIGR00461 139 aeamalsfrvskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdG 207
aeamal++rv+k+k+n f+v++++hpqtl+vv+tra ++g+e++vd + ++ ++ +v+G+llqyp ++G
lcl|NCBI__GCF_900100495.1:WP_090443896.1 157 AEAMALAKRVAKSKSNLFFVDENCHPQTLSVVQTRAAAFGFELVVDAVANLGQH-QVFGALLQYPDSHG 224
*******************************************99988888776.6************* PP
TIGR00461 208 eildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdey 276
ei d++ li +l+ ++al +va+dll+l lltppg+lGad+++GsaqrfGvp+GyGGphaaffa++de+
lcl|NCBI__GCF_900100495.1:WP_090443896.1 225 EIRDLRPLIAQLHAQQALACVACDLLSLLLLTPPGELGADVAFGSAQRFGVPMGYGGPHAAFFATRDEF 293
********************************************************************* PP
TIGR00461 277 krklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlkniar 345
kr +pGri+Gvskda Gn alr+alqtreqhirr+ka+snictaqvllan+a yavyhGp Glk+ia+
lcl|NCBI__GCF_900100495.1:WP_090443896.1 294 KRAMPGRIIGVSKDARGNVALRMALQTREQHIRREKANSNICTAQVLLANIAGFYAVYHGPEGLKRIAQ 362
********************************************************************* PP
TIGR00461 346 rifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdettt 414
r++rlt++laagl +++ n ++fdtlt+evg + ++ ++a++a inlr + +++g++ldet
lcl|NCBI__GCF_900100495.1:WP_090443896.1 363 RVHRLTALLAAGLAQNGIARDNRHFFDTLTLEVGGSQT-AIIESAQAARINLRILGRGKLGVSLDETCD 430
*********************************98776.89999************************* PP
TIGR00461 415 kedvldllkvlagkdnlglsseelse.dvansfpaellrddeilrdevfnryhsetellrylhrleskd 482
++ ++ l+ +++g d +gls+ +l+e ++ +p+el r++ +lr++vfn +hsete+lryl++le+kd
lcl|NCBI__GCF_900100495.1:WP_090443896.1 431 EHTLMRLFAIFLGAD-HGLSVTKLDEgEIGGGIPSELARSSAYLRHPVFNSHHSETEMLRYLKQLENKD 498
*************87.********9846778************************************** PP
TIGR00461 483 lalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaislq 551
lalnq+miplGsctmklna+ em+pitwp+fa++hpf p eq++Gy+ li +le+wl itGfdai++q
lcl|NCBI__GCF_900100495.1:WP_090443896.1 499 LALNQAMIPLGSCTMKLNASSEMIPITWPQFADLHPFVPVEQAQGYRLLIDELEAWLRAITGFDAICMQ 567
********************************************************************* PP
TIGR00461 552 pnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlka 620
pnsGaqGeyaGl +ir+yh+srg+ +rn+clipasahGtnpasa+ma l++v v+cd +Gn+dl dlk
lcl|NCBI__GCF_900100495.1:WP_090443896.1 568 PNSGAQGEYAGLLAIRKYHDSRGDSQRNVCLIPASAHGTNPASAQMASLRIVIVECDSHGNVDLDDLKR 636
********************************************************************* PP
TIGR00461 621 kaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnl 689
ka +ag++la++m+typst+Gv+ee+ire++++vh GGqvy+dGan+naqvGlt+p+d+Gadv+h+nl
lcl|NCBI__GCF_900100495.1:WP_090443896.1 637 KALEAGEQLACLMITYPSTHGVYEEGIREICEVVHAQGGQVYMDGANLNAQVGLTRPADIGADVSHMNL 705
********************************************************************* PP
TIGR00461 690 hktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikm 758
hktf+iphGGGGpgmgpigvk+hlapf+ + + v+el+g + + gavs ap+Gsasilpis+myi+m
lcl|NCBI__GCF_900100495.1:WP_090443896.1 706 HKTFCIPHGGGGPGMGPIGVKAHLAPFVAN---HPVIELQGPDPQNGAVSGAPWGSASILPISWMYIAM 771
******************************...899********************************* PP
TIGR00461 759 mGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyG 827
mG++ l asevail+anyla++l a+++l+ gr++rvahecildlr+lk+++gi+++dvakrl+dyG
lcl|NCBI__GCF_900100495.1:WP_090443896.1 772 MGPQ-LADASEVAILSANYLAQQLGGAFPLLYSGRNGRVAHECILDLRPLKAQTGISEEDVAKRLMDYG 839
***8.99************************************************************** PP
TIGR00461 828 fhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqsliva 896
fhapt+sfpv+Gtlm+epteses++eldrfi+am++i++ei +v +G++++edn+lk aph+l ++ ++
lcl|NCBI__GCF_900100495.1:WP_090443896.1 840 FHAPTMSFPVPGTLMIEPTESESKHELDRFIEAMLSIRAEIAKVHSGDWPAEDNPLKRAPHTLADV-IG 907
*************************************************************99885.58 PP
TIGR00461 897 ewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
w pys e+a+ p + + +k+wptv+r+d++yGdrnl+c+c
lcl|NCBI__GCF_900100495.1:WP_090443896.1 908 VWERPYSLEQAVTPTAHSRAHKYWPTVNRVDNVYGDRNLFCAC 950
9*****************************************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (958 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: 0.08u 0.02s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 9.56
//
[ok]
This GapMind analysis is from Sep 24 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