Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate 7026357 Shewana3_3499 glycine dehydrogenase (RefSeq)
Query= CharProtDB::CH_003480
(957 letters)
>FitnessBrowser__ANA3:7026357
Length = 962
Score = 1350 bits (3494), Expect = 0.0
Identities = 660/960 (68%), Positives = 796/960 (82%), Gaps = 6/960 (0%)
Query: 3 QTLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAPA 62
QTL+QLE F+ RHIGPD++QQQEMLN VGA+SL+ LT QIVP+ I+L+ +G
Sbjct: 4 QTLTQLEQHDLFLRRHIGPDSSQQQEMLNYVGAESLDDLTAQIVPESIRLSQELSIGDSC 63
Query: 63 TEYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQG 122
E +A ++ +A +N+ F SYIGMGY Q+P VILRN+ ENPGWYTAYTPYQPE++QG
Sbjct: 64 GEAEGIAYIRGLAKQNQVFKSYIGMGYYGTQVPNVILRNVFENPGWYTAYTPYQPEIAQG 123
Query: 123 RLEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHPQ 182
RLEA+LNFQQV++DLTGLD+ASASLLDEATAAAEAMA+AKRVSK K AN FFVA DV PQ
Sbjct: 124 RLEAILNFQQVSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKKANIFFVADDVFPQ 183
Query: 183 TLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKIV 242
TLDVV+TRAE FGFEV+V A + ++H+ +FG L Q G+I D+T L +EL+++ ++
Sbjct: 184 TLDVVKTRAECFGFEVVVGPAHEAVNHE-LFGALFQYSNRFGQITDFTDLFAELRAKNVI 242
Query: 243 VSVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRII 302
V+VAADIMALVLL +PG GAD+VFGSAQRFGVPMG+GGPHAAFF A+DE+KRSMPGRII
Sbjct: 243 VTVAADIMALVLLKSPGAMGADVVFGSAQRFGVPMGFGGPHAAFFVARDEHKRSMPGRII 302
Query: 303 GVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIAN 362
GVSKD GN ALRMAMQTREQHIRREKANSNICT+Q+LLAN+AS YAV+HGP GLK IA+
Sbjct: 303 GVSKDTRGNRALRMAMQTREQHIRREKANSNICTAQILLANMASFYAVFHGPQGLKTIAS 362
Query: 363 RIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVADKAGVLTRAEAAEINLRSDILNAVGI 422
RI+R TDILAAGLQ KG+ L + +FDT+ ++ D A V RA AAE+NLR D VG+
Sbjct: 363 RINRFTDILAAGLQAKGVSLVNNTWFDTISIKGLDVAAVNARALAAEMNLRFDADGIVGV 422
Query: 423 TLDETTTRENVMQLFNVLLGDNHGLDIDTLDKD-VAHDSRSIQPAMLRDDEILTHPVFNR 481
+LDETT R ++ LF+V+LG HGLD+ LD VA S+SI +++R D IL+HP FNR
Sbjct: 423 SLDETTIRTDIEALFDVILGAGHGLDVAALDAQIVAQGSQSIPASLVRQDAILSHPTFNR 482
Query: 482 YHSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPEQ 541
Y SETEMMRY+ LE KDLALN +MI LGSCTMKLNAA EMIP++WPEFA +HPFCP +Q
Sbjct: 483 YQSETEMMRYIKRLESKDLALNYSMISLGSCTMKLNAAVEMIPVSWPEFANMHPFCPLDQ 542
Query: 542 AEGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIP 601
A+GY Q+I +L+ WLV +TGYDAVC+QPNSGAQGEYAGLLAIR YHESR E HR+ICLIP
Sbjct: 543 AKGYTQLIEELSSWLVNVTGYDAVCIQPNSGAQGEYAGLLAIRKYHESRGEAHRNICLIP 602
Query: 602 ASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVYE 661
SAHGTNPASA +AGMQVVV ACDK GN+DL DL+AKA + +NLSCIM+TYPSTHGVYE
Sbjct: 603 QSAHGTNPASAQLAGMQVVVTACDKQGNVDLEDLKAKAAEVAENLSCIMITYPSTHGVYE 662
Query: 662 ETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGM 721
E+IRE+C +VHQ GGQVYLDGANMNAQVG+TSPGFIGADVSHLNLHKTF IPHGGGGPGM
Sbjct: 663 ESIREICNIVHQHGGQVYLDGANMNAQVGLTSPGFIGADVSHLNLHKTFAIPHGGGGPGM 722
Query: 722 GPIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKKA 781
GPIGVKAHLAPFV GH VV+ GAVSAAP+GSA ILPISWMYI+++G+ GLKK+
Sbjct: 723 GPIGVKAHLAPFVAGHVVVKPGRESDNNGAVSAAPYGSAGILPISWMYIKLLGSNGLKKS 782
Query: 782 SQVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDYG 841
+Q A+LNANY+ +L + +PVL+ GR+ RVAHECI+D+RP+KE +G++E+DIAKRL DYG
Sbjct: 783 TQTALLNANYVMKKLSEHYPVLFRGRNDRVAHECIIDLRPIKEASGVTEMDIAKRLNDYG 842
Query: 842 FHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNAP 901
FHAPTMSFPVAGTLM+EPTESESKVELDRFIDAM++IRAEI +V+AG WP ++NPL NAP
Sbjct: 843 FHAPTMSFPVAGTLMIEPTESESKVELDRFIDAMVSIRAEIAKVEAGEWPADNNPLHNAP 902
Query: 902 HIQSELV--AEWAHPYSREVAVFPAGV--ADKYWPTVKRLDDVYGDRNLFCSCVPISEYQ 957
H ++++ A + PYSREVAVFP+ +K+WPTV R+DDVYGDRNLFC+CVP+S+Y+
Sbjct: 903 HTMADIMDPAFDSRPYSREVAVFPSAAVRTNKFWPTVNRIDDVYGDRNLFCACVPLSDYE 962
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: 2277
Number of extensions: 71
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: 962
Length adjustment: 44
Effective length of query: 913
Effective length of database: 918
Effective search space: 838134
Effective search space used: 838134
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 7026357 Shewana3_3499 (glycine dehydrogenase (RefSeq))
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.25062.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 1535.1 0.1 0 1535.0 0.1 1.0 1 lcl|FitnessBrowser__ANA3:7026357 Shewana3_3499 glycine dehydrogen
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026357 Shewana3_3499 glycine dehydrogenase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1535.0 0.1 0 0 1 939 [] 18 955 .. 18 955 .. 0.98
Alignments for each domain:
== domain 1 score: 1535.0 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyati 77
rh+Gpd+++q++ml+ +G+++l++l+ q+vp++irl++ l ++ + e e +a ++ +a++n+++ksyiG+Gyy+t+
lcl|FitnessBrowser__ANA3:7026357 18 RHIGPDSSQQQEMLNYVGAESLDDLTAQIVPESIRLSQELSIGDSCGEAEGIAYIRGLAKQNQVFKSYIGMGYYGTQ 94
9**************************************************************************** PP
TIGR00461 78 lppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk.a 153
+p vi+rn++enpgwytaytpyqpei+qGrlea+lnfq+v +dltGl++a+asllde+taaaeamal++rvsk k a
lcl|FitnessBrowser__ANA3:7026357 95 VPNVILRNVFENPGWYTAYTPYQPEIAQGRLEAILNFQQVSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKkA 171
*************************************************************************8879 PP
TIGR00461 154 nkfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaa 230
n f+va+dv pqtl+vvktrae +g+ev+v+ a++ ++ +++G+l qy+ G+i d+++l el+ ++++v+vaa
lcl|FitnessBrowser__ANA3:7026357 172 NIFFVADDVFPQTLDVVKTRAECFGFEVVVGPAHEAVNH-ELFGALFQYSNRFGQITDFTDLFAELRAKNVIVTVAA 247
9*********************************98765.89*********************************** PP
TIGR00461 231 dllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqh 307
d++al+ll++pg +Gad+v+GsaqrfGvp+G+GGphaaff ++de+kr++pGri+Gvskd+ Gn alr+a+qtreqh
lcl|FitnessBrowser__ANA3:7026357 248 DIMALVLLKSPGAMGADVVFGSAQRFGVPMGFGGPHAAFFVARDEHKRSMPGRIIGVSKDTRGNRALRMAMQTREQH 324
***************************************************************************** PP
TIGR00461 308 irrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaas 384
irr+ka+snictaq+llan+as yav+hGp+Glk ia ri r+t+ilaagl+ k+ +l n+t+fdt++++ + aa
lcl|FitnessBrowser__ANA3:7026357 325 IRREKANSNICTAQILLANMASFYAVFHGPQGLKTIASRINRFTDILAAGLQAKGVSLVNNTWFDTISIKGLDVAA- 400
**********************************************************************998888. PP
TIGR00461 385 evlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan....sfpaellrddeil 457
v+ +a +ae+nlr + + vg++ldett + d++ l++v++g +gl++ l+ ++ s+pa l r+d il
lcl|FitnessBrowser__ANA3:7026357 401 -VNARALAAEMNLRFDADGIVGVSLDETTIRTDIEALFDVILG-AGHGLDVAALDAQIVAqgsqSIPASLVRQDAIL 475
.9*****************************************.55*******99987544666************* PP
TIGR00461 458 rdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaq 534
++ fnry sete++ry++rleskdlaln smi lGsctmklna++em+p++wpefa++hpf+p +q++Gy +li +
lcl|FitnessBrowser__ANA3:7026357 476 SHPTFNRYQSETEMMRYIKRLESKDLALNYSMISLGSCTMKLNAAVEMIPVSWPEFANMHPFCPLDQAKGYTQLIEE 552
***************************************************************************** PP
TIGR00461 535 lekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeG 611
l +wlv++tG+da+++qpnsGaqGeyaGl +ir+yhesrge hrniclip+sahGtnpasa++aG++vv+ +cdk+G
lcl|FitnessBrowser__ANA3:7026357 553 LSSWLVNVTGYDAVCIQPNSGAQGEYAGLLAIRKYHESRGEAHRNICLIPQSAHGTNPASAQLAGMQVVVTACDKQG 629
***************************************************************************** PP
TIGR00461 612 nidlvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchln 688
n+dl+dlkaka + +++l+++m+typst+Gv+ee+ire+++ivh+ GGqvyldGanmnaqvGltspg++Gadv+hln
lcl|FitnessBrowser__ANA3:7026357 630 NVDLEDLKAKAAEVAENLSCIMITYPSTHGVYEESIREICNIVHQHGGQVYLDGANMNAQVGLTSPGFIGADVSHLN 706
***************************************************************************** PP
TIGR00461 689 lhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlk 765
lhktf+iphGGGGpgmgpigvk+hlapf+ + + vv+ es + gavsaapyGsa ilpis+myik++G++Glk
lcl|FitnessBrowser__ANA3:7026357 707 LHKTFAIPHGGGGPGMGPIGVKAHLAPFVAG---HVVVKPGRESDNNGAVSAAPYGSAGILPISWMYIKLLGSNGLK 780
*******************************...67788889999******************************** PP
TIGR00461 766 kasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlm 842
k+++ a+lnany++k+l ++y++lf+gr++rvaheci+dlr++ke +g+ ++d+akrl dyGfhapt+sfpvaGtlm
lcl|FitnessBrowser__ANA3:7026357 781 KSTQTALLNANYVMKKLSEHYPVLFRGRNDRVAHECIIDLRPIKEASGVTEMDIAKRLNDYGFHAPTMSFPVAGTLM 857
***************************************************************************** PP
TIGR00461 843 veptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaew.adpysreeaaypapvlkyfk 918
+epteses++eldrfidam++i++ei +v aGe+++++n+l+naph++ + + + pysre+a++p + ++ +k
lcl|FitnessBrowser__ANA3:7026357 858 IEPTESESKVELDRFIDAMVSIRAEIAKVEAGEWPADNNPLHNAPHTMADIMDPAFdSRPYSREVAVFPSAAVRTNK 934
*************************************************99987661567***************** PP
TIGR00461 919 fwptvarlddtyGdrnlvcsc 939
fwptv+r+dd+yGdrnl+c+c
lcl|FitnessBrowser__ANA3:7026357 935 FWPTVNRIDDVYGDRNLFCAC 955
********************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (962 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 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 8.85
//
[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