Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate GFF182 Psest_0183 glycine dehydrogenase (decarboxylating)
Query= CharProtDB::CH_003480
(957 letters)
>FitnessBrowser__psRCH2:GFF182
Length = 958
Score = 1256 bits (3251), Expect = 0.0
Identities = 625/957 (65%), Positives = 752/957 (78%), Gaps = 8/957 (0%)
Query: 4 TLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPAT 63
+LSQL+ AF+ RH+GPD A+QQ ML+A+G S L Q VP I+L + A
Sbjct: 6 SLSQLQQPDAFLRRHLGPDQAEQQAMLDALGLTSREQLIEQTVPPAIRLQDELDLPAALD 65
Query: 64 EYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQGR 123
E AALA+L+ A +N+ +TS IGMGY PPVILRN+LENPGWYTAYTPYQPE++QGR
Sbjct: 66 EQAALAKLRGYAEQNQLWTSLIGMGYHGTITPPVILRNVLENPGWYTAYTPYQPEIAQGR 125
Query: 124 LEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHPQT 183
LEALLN+QQ+ +DLTGLD+A+ASLLDEATAAAEAM +A+R++K K+ NRFFV + HPQT
Sbjct: 126 LEALLNYQQMIIDLTGLDLANASLLDEATAAAEAMTLARRMAKSKS-NRFFVDENCHPQT 184
Query: 184 LDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIVV 243
L VV+TRAE FGFE++V + L Q+VFG LLQ T GEI D I +L +++ +
Sbjct: 185 LSVVQTRAEAFGFELVVGTLDE-LAGQEVFGALLQYPDTHGEIRDLRPAIEQLHAQQALA 243
Query: 244 SVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRIIG 303
VAAD+++L+LLT PG+ GAD+V GS QRFGVPMGYGGPHAA+FA++DE+KR MPGRIIG
Sbjct: 244 CVAADLLSLLLLTPPGELGADVVLGSTQRFGVPMGYGGPHAAYFASRDEFKRGMPGRIIG 303
Query: 304 VSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIANR 363
VSKDA GNTALRMA+QTREQHIRREKANSNICT+QVLLANIA YAVYHGP GLKRIA R
Sbjct: 304 VSKDARGNTALRMALQTREQHIRREKANSNICTAQVLLANIAGFYAVYHGPQGLKRIAQR 363
Query: 364 IHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVAD-KAGVLTRAEAAEINLRSDILNAVGI 422
+HRLT ILAAGL+QKG+ + H+FDTL +EV + ++ AEAA+INLR +G+
Sbjct: 364 VHRLTAILAAGLEQKGIVRLNQHFFDTLTLEVGGAQTAIIESAEAAQINLRILGRGRLGV 423
Query: 423 TLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDVAHDSRSIQPAMLRDDEILTHPVFNRY 482
+LDET V QL + LG +HGLD+ LD + I + R+ L HPVFN +
Sbjct: 424 SLDETCDERTVEQLLAIFLGADHGLDVAALD--AGELAAGIPAGLQRESGYLEHPVFNSH 481
Query: 483 HSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPEQA 542
HSETEM+RY+ LE KDLALNQAMIPLGSCTMKLNA +EMIPITW EFA LHPF P QA
Sbjct: 482 HSETEMLRYLKQLENKDLALNQAMIPLGSCTMKLNATSEMIPITWAEFANLHPFVPRVQA 541
Query: 543 EGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIPA 602
+GY+ MI +L WL +TG+DA+ MQPNSGAQGEYAGL+AIR YHESR EG RDICLIP+
Sbjct: 542 QGYKLMIEELEAWLCAITGFDAISMQPNSGAQGEYAGLVAIRKYHESRGEGQRDICLIPS 601
Query: 603 SAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVYEE 662
SAHGTNPASA M M+VV+V CDK GN+DL DL+ KA +AGD LSC+M+TYPSTHGVYEE
Sbjct: 602 SAHGTNPASAQMVSMRVVIVECDKGGNVDLEDLKRKAAEAGDRLSCLMITYPSTHGVYEE 661
Query: 663 TIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGMG 722
+RE+C +H GGQVY+DGAN+NAQVG+ P IGADVSH+NLHKTFCIPHGGGGPGMG
Sbjct: 662 NVREICAAIHAHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMG 721
Query: 723 PIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKAS 782
PIGVKAHLAPFV H VV++EG GAVSAAP+GSASILPISWMYI MMG + L+ A+
Sbjct: 722 PIGVKAHLAPFVANHPVVELEGPQPGNGAVSAAPWGSASILPISWMYIAMMGPQ-LRDAT 780
Query: 783 QVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDYGF 842
+VAIL ANY+A+RL DAFPVLY GR+GRVAHECILD+RPLK +GISE D+AKRL+DYGF
Sbjct: 781 EVAILGANYLANRLGDAFPVLYAGRNGRVAHECILDLRPLKAASGISEEDVAKRLMDYGF 840
Query: 843 HAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNAPH 902
HAPTMSFPV GTLM+EPTESESK ELDRF++AML+IRAEI +V+ G WP ++NPLV APH
Sbjct: 841 HAPTMSFPVPGTLMIEPTESESKAELDRFVEAMLSIRAEIAKVQDGEWPADNNPLVRAPH 900
Query: 903 IQSELVAEWAHPYSREVAVFPA--GVADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
++++ EW PYS AV P+ A KYWP V R+D+VYGDRNLFC+CVP+ Y+
Sbjct: 901 TLADVIGEWDRPYSIAEAVTPSAHARAHKYWPAVNRVDNVYGDRNLFCACVPVDAYR 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: 2289
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: 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 GFF182 Psest_0183 (glycine dehydrogenase (decarboxylating))
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.24950.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 1535.7 0.0 0 1535.5 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF182 Psest_0183 glycine dehydrogenase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF182 Psest_0183 glycine dehydrogenase (decarboxylating)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1535.5 0.0 0 0 1 939 [] 19 950 .. 19 950 .. 0.99
Alignments for each domain:
== domain 1 score: 1535.5 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyat 76
rhlGpd+aeq+ ml++lG + ++lieq vp++irl+ l l+a+ e++ala+l+ a++n+ +s iG+Gy +t
lcl|FitnessBrowser__psRCH2:GFF182 19 RHLGPDQAEQQAMLDALGLTSREQLIEQTVPPAIRLQDELDLPAALDEQAALAKLRGYAEQNQLWTSLIGMGYHGT 94
9*************************************************************************** PP
TIGR00461 77 ilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk 152
i+ppvi+rn+lenpgwytaytpyqpei+qGrlealln+q++++dltGl++anasllde+taaaeam l+ r++k+k
lcl|FitnessBrowser__psRCH2:GFF182 95 ITPPVILRNVLENPGWYTAYTPYQPEIAQGRLEALLNYQQMIIDLTGLDLANASLLDEATAAAEAMTLARRMAKSK 170
**************************************************************************** PP
TIGR00461 153 ankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsv 228
+n+f+v++++hpqtl+vv+trae++g+e++v+ +++ ++v+G+llqyp t+Gei d++ i++l+ ++al +v
lcl|FitnessBrowser__psRCH2:GFF182 171 SNRFFVDENCHPQTLSVVQTRAEAFGFELVVGTLDELA-GQEVFGALLQYPDTHGEIRDLRPAIEQLHAQQALACV 245
*******************************9998875.789********************************** PP
TIGR00461 229 aadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtr 304
aadll+l lltppg+lGad+vlGs+qrfGvp+GyGGphaa+fa++de+kr +pGri+Gvskda Gntalr+alqtr
lcl|FitnessBrowser__psRCH2:GFF182 246 AADLLSLLLLTPPGELGADVVLGSTQRFGVPMGYGGPHAAYFASRDEFKRGMPGRIIGVSKDARGNTALRMALQTR 321
**************************************************************************** PP
TIGR00461 305 eqhirrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevge 380
eqhirr+ka+snictaqvllan+a yavyhGp+Glk+ia+r++rlt+ilaagl++k+ n+++fdtlt+evg
lcl|FitnessBrowser__psRCH2:GFF182 322 EQHIRREKANSNICTAQVLLANIAGFYAVYHGPQGLKRIAQRVHRLTAILAAGLEQKGIVRLNQHFFDTLTLEVGG 397
**************************************************************************98 PP
TIGR00461 381 kaasevlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelse.dvansfpaellrdde 455
+ ++ ++ae+a+inlr + + +g++ldet ++ v++ll +++g d +gl++ l+ ++a +pa l+r++
lcl|FitnessBrowser__psRCH2:GFF182 398 AQT-AIIESAEAAQINLRILGRGRLGVSLDETCDERTVEQLLAIFLGAD-HGLDVAALDAgELAAGIPAGLQRESG 471
776.8999***************************************87.********8648999*********** PP
TIGR00461 456 ilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykel 531
+l+++vfn +hsete+lryl++le+kdlalnq+miplGsctmklnat em+pitw efa++hpf p q++Gyk +
lcl|FitnessBrowser__psRCH2:GFF182 472 YLEHPVFNSHHSETEMLRYLKQLENKDLALNQAMIPLGSCTMKLNATSEMIPITWAEFANLHPFVPRVQAQGYKLM 547
**************************************************************************** PP
TIGR00461 532 iaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkc 607
i +le+wl+ itGfdais+qpnsGaqGeyaGl +ir+yhesrge++r+iclip sahGtnpasa+m+ ++vv v+c
lcl|FitnessBrowser__psRCH2:GFF182 548 IEELEAWLCAITGFDAISMQPNSGAQGEYAGLVAIRKYHESRGEGQRDICLIPSSAHGTNPASAQMVSMRVVIVEC 623
**************************************************************************** PP
TIGR00461 608 dkeGnidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGad 683
dk Gn+dl+dlk ka +agd+l+++m+typst+Gv+ee +re++ +h GGqvy+dGan+naqvGl++p+d+Gad
lcl|FitnessBrowser__psRCH2:GFF182 624 DKGGNVDLEDLKRKAAEAGDRLSCLMITYPSTHGVYEENVREICAAIHAHGGQVYMDGANLNAQVGLARPADIGAD 699
**************************************************************************** PP
TIGR00461 684 vchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmm 759
v+h+nlhktf+iphGGGGpgmgpigvk+hlapf+ + + vveleg + gavsaap+Gsasilpis+myi+mm
lcl|FitnessBrowser__psRCH2:GFF182 700 VSHMNLHKTFCIPHGGGGPGMGPIGVKAHLAPFVAN---HPVVELEGPQPGNGAVSAAPWGSASILPISWMYIAMM 772
************************************...8899********************************* PP
TIGR00461 760 GaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsf 835
G++ l+ a+evail anyla+rl da+++l+ gr++rvahecildlr+lk+ +gi+++dvakrl+dyGfhapt+sf
lcl|FitnessBrowser__psRCH2:GFF182 773 GPQ-LRDATEVAILGANYLANRLGDAFPVLYAGRNGRVAHECILDLRPLKAASGISEEDVAKRLMDYGFHAPTMSF 847
**8.9*********************************************************************** PP
TIGR00461 836 pvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaaypa 911
pv+Gtlm+epteses+ eldrf++am++i++ei +v+ Ge+++++n+l+ aph+l ++ ++ew pys ea+ p
lcl|FitnessBrowser__psRCH2:GFF182 848 PVPGTLMIEPTESESKAELDRFVEAMLSIRAEIAKVQDGEWPADNNPLVRAPHTLADV-IGEWDRPYSIAEAVTPS 922
*****************************************************99875.69*************** PP
TIGR00461 912 pvlkyfkfwptvarlddtyGdrnlvcsc 939
+ ++ +k+wp+v+r+d++yGdrnl+c+c
lcl|FitnessBrowser__psRCH2:GFF182 923 AHARAHKYWPAVNRVDNVYGDRNLFCAC 950
***************************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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 12.41
//
[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