Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate WP_046011132.1 OLEAN_RS13085 glycine dehydrogenase (aminomethyl-transferring)
Query= CharProtDB::CH_003480
(957 letters)
>NCBI__GCF_000967895.1:WP_046011132.1
Length = 964
Score = 1217 bits (3149), Expect = 0.0
Identities = 597/962 (62%), Positives = 743/962 (77%), Gaps = 7/962 (0%)
Query: 2 TQTLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAP 61
TQTL QLE FI RHIGPDA++++ +L AVGA SL L+ QIVP DI ++
Sbjct: 3 TQTLVQLEQRDNFIGRHIGPDASEEKALLEAVGATSLEDLSTQIVPADILREEFLEIADG 62
Query: 62 ATEYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQ 121
TE+ A+ L+++A +NK F SYIGMGY +PPVILRN+LENPGWYTAYTPYQPE++Q
Sbjct: 63 RTEFEAINYLRSLADQNKVFKSYIGMGYNDTIVPPVILRNVLENPGWYTAYTPYQPEIAQ 122
Query: 122 GRLEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHP 181
GRLEALLNFQQ+ D+TG+++A+ASLLDE TAAAEAMAM KR + +N FFV + P
Sbjct: 123 GRLEALLNFQQLVCDMTGMELANASLLDEGTAAAEAMAMTKRTVRKNKSNTFFVDENCLP 182
Query: 182 QTLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKI 241
QT+DV++TRAE FG+EVI+ A + D DVFG + Q G G + D+T +I+ L ++
Sbjct: 183 QTIDVIKTRAEAFGWEVIIAPAAQAAD-ADVFGAIFQYPGKGGNVEDFTDIITALHAKDA 241
Query: 242 VVSVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRI 301
+ +VA D+MALV L P + GADIV G+AQ FGVPMG+GGPHAAFFA KD+YKRS+PGRI
Sbjct: 242 LATVATDLMALVALKTPAEMGADIVLGNAQHFGVPMGFGGPHAAFFATKDKYKRSIPGRI 301
Query: 302 IGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIA 361
IGVS DA GN ALRMA+QTREQHIRREKANSNICT+Q LLAN++S YAVYHGP GLK IA
Sbjct: 302 IGVSIDAQGNQALRMALQTREQHIRREKANSNICTAQALLANLSSFYAVYHGPQGLKTIA 361
Query: 362 NRIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVADKAGVLTRAEAAEINLRSDILNAVG 421
RIHRLTDILA GL++ G+KL + +FDTL V D+ V+ RA AAE+NLR D VG
Sbjct: 362 GRIHRLTDILALGLKKAGIKLANDTWFDTLTVITDDRDAVIHRALAAEVNLRLDSAVTVG 421
Query: 422 ITLDETTTRENVMQLFNVLLGD---NHGLDIDTLDKDV-AHDSRSIQPAMLRDDEILTHP 477
+++ E T+ ++ +LF + LGD + LDI LD +V A D+ SI ++R E LTHP
Sbjct: 422 VSICEKTSAADIAELFTIFLGDAAEDFNLDIYELDAEVVAADATSIPADLIRTTEFLTHP 481
Query: 478 VFNRYHSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFC 537
FN YHSE EM+RYM SLE KDLA+N +MI LGSCTMKLNA +MIP++WPEF+ +HPF
Sbjct: 482 TFNSYHSEHEMLRYMKSLEVKDLAMNHSMITLGSCTMKLNATTQMIPLSWPEFSTIHPFA 541
Query: 538 PPEQAEGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDI 597
P +Q GY++MI +L D+L +TG+ A+CMQPNSGAQGEYAGL+AI+ YHESR EGHR++
Sbjct: 542 PKDQTIGYEKMIDELDDYLKDITGFSAICMQPNSGAQGEYAGLIAIKKYHESRGEGHRNV 601
Query: 598 CLIPASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTH 657
CLIP SAHGTNPASA MA M+VVV CD+ GN+D DL+AKAE+ GDNLSC+M+TYPSTH
Sbjct: 602 CLIPRSAHGTNPASAQMASMKVVVTNCDELGNVDFADLKAKAEEIGDNLSCLMITYPSTH 661
Query: 658 GVYEETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGG 717
GVYEE I+E+CE+VH GGQVY+DGAN+NAQVGIT P ++GADVSH+NLHKTF IPHGGG
Sbjct: 662 GVYEEGIKEICELVHSLGGQVYMDGANLNAQVGITQPAYLGADVSHMNLHKTFAIPHGGG 721
Query: 718 GPGMGPIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEG 777
GPGMGPIGV AHL PFV H+V I+ QGAVS+AP+GSASIL ISWMYI +MG +G
Sbjct: 722 GPGMGPIGVAAHLEPFVANHAVRPIDNESKGQGAVSSAPYGSASILTISWMYITLMGGKG 781
Query: 778 LKKASQVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRL 837
L+KA+Q A+L ANY+A RL + +P+LY+G G VAHECI+D+RPLKE+TGI+E+DIAKRL
Sbjct: 782 LRKATQHALLKANYLAKRLGEHYPILYSGNKGLVAHECIIDLRPLKEQTGITEVDIAKRL 841
Query: 838 IDYGFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPL 897
+DYGFHAPTMSFPVAGT M+EPTESESK E+DRF +AM++I+ EI + G E+NPL
Sbjct: 842 MDYGFHAPTMSFPVAGTFMIEPTESESKAEIDRFANAMISIKGEIMAIHNGELDAENNPL 901
Query: 898 VNAPHIQSELVAEWAHPYSREVAVFPAG--VADKYWPTVKRLDDVYGDRNLFCSCVPISE 955
NAPH + + +W PYS+++A FP A K+WP+V R+DDVYGDRNL CSC I
Sbjct: 902 KNAPHTAAVVTGDWDRPYSQQLAAFPTKNLGAHKFWPSVGRIDDVYGDRNLICSCPAIEN 961
Query: 956 YQ 957
Y+
Sbjct: 962 YE 963
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: 2161
Number of extensions: 81
Number of successful extensions: 4
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: 964
Length adjustment: 44
Effective length of query: 913
Effective length of database: 920
Effective search space: 839960
Effective search space used: 839960
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_046011132.1 OLEAN_RS13085 (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.635.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 1488.7 0.4 0 1488.6 0.4 1.0 1 lcl|NCBI__GCF_000967895.1:WP_046011132.1 OLEAN_RS13085 glycine dehydrogen
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000967895.1:WP_046011132.1 OLEAN_RS13085 glycine dehydrogenase (aminomethyl-transferring)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1488.6 0.4 0 0 1 939 [] 18 956 .. 18 956 .. 0.98
Alignments for each domain:
== domain 1 score: 1488.6 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyi 69
rh+Gpd++e k +l+++G+ +l++l q+vp di+ + l++ +e+ea++ l+++a++nk++ksyi
lcl|NCBI__GCF_000967895.1:WP_046011132.1 18 RHIGPDASEEKALLEAVGATSLEDLSTQIVPADILREEFLEIADGRTEFEAINYLRSLADQNKVFKSYI 86
9******************************************************************** PP
TIGR00461 70 GkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaa 138
G+Gy +ti+ppvi+rn+lenpgwytaytpyqpei+qGrleallnfq++v d+tG+e+anaslldegtaa
lcl|NCBI__GCF_000967895.1:WP_046011132.1 87 GMGYNDTIVPPVILRNVLENPGWYTAYTPYQPEIAQGRLEALLNFQQLVCDMTGMELANASLLDEGTAA 155
********************************************************************* PP
TIGR00461 139 aeamalsfr.vskkkankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatd 206
aeama+++r v k+k+n f+v++++ pqt++v+ktrae++g evi+ a + + dv+G++ qyp+
lcl|NCBI__GCF_000967895.1:WP_046011132.1 156 AEAMAMTKRtVRKNKSNTFFVDENCLPQTIDVIKTRAEAFGWEVIIAPAAQAAD-ADVFGAIFQYPGKG 223
******997366778********************************9998765.69************ PP
TIGR00461 207 GeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkde 275
G++ d++++i +l+ + al +va+dl+al+ l++p+++GadivlG aq fGvp+G+GGphaaffa+kd+
lcl|NCBI__GCF_000967895.1:WP_046011132.1 224 GNVEDFTDIITALHAKDALATVATDLMALVALKTPAEMGADIVLGNAQHFGVPMGFGGPHAAFFATKDK 292
********************************************************************* PP
TIGR00461 276 ykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlknia 344
ykr++pGri+Gvs da+Gn alr+alqtreqhirr+ka+snictaq+llan++s yavyhGp+Glk ia
lcl|NCBI__GCF_000967895.1:WP_046011132.1 293 YKRSIPGRIIGVSIDAQGNQALRMALQTREQHIRREKANSNICTAQALLANLSSFYAVYHGPQGLKTIA 361
********************************************************************* PP
TIGR00461 345 rrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdett 413
ri+rlt+ila glk+ + +l n+t+fdtltv ++ a v ++a +ae+nlr + + +vg+++ e t
lcl|NCBI__GCF_000967895.1:WP_046011132.1 362 GRIHRLTDILALGLKKAGIKLANDTWFDTLTVITDDRDA--VIHRALAAEVNLRLDSAVTVGVSICEKT 428
********************************9888887..999999********************** PP
TIGR00461 414 tkedvldllkvlagk..dnlglsseelsedvan....sfpaellrddeilrdevfnryhsetellrylh 476
+ +d+ +l+ +++g+ ++++l++ el+ +v s+pa+l r+ e+l+++ fn yhse e+lry++
lcl|NCBI__GCF_000967895.1:WP_046011132.1 429 SAADIAELFTIFLGDaaEDFNLDIYELDAEVVAadatSIPADLIRTTEFLTHPTFNSYHSEHEMLRYMK 497
************9862245677888999998655666******************************** PP
TIGR00461 477 rleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGf 545
+le kdla+n+smi lGsctmklnat++m+p++wpef+ ihpfap +q+ Gy+++i +l+++l +itGf
lcl|NCBI__GCF_000967895.1:WP_046011132.1 498 SLEVKDLAMNHSMITLGSCTMKLNATTQMIPLSWPEFSTIHPFAPKDQTIGYEKMIDELDDYLKDITGF 566
********************************************************************* PP
TIGR00461 546 daislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnid 614
ai++qpnsGaqGeyaGl +i++yhesrge+hrn+clip sahGtnpasa+ma +kvv+ +cd+ Gn+d
lcl|NCBI__GCF_000967895.1:WP_046011132.1 567 SAICMQPNSGAQGEYAGLIAIKKYHESRGEGHRNVCLIPRSAHGTNPASAQMASMKVVVTNCDELGNVD 635
********************************************************************* PP
TIGR00461 615 lvdlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGad 683
+ dlkakae+ gd+l+++m+typst+Gv+ee+i+e++++vh++GGqvy+dGan+naqvG+t+p++lGad
lcl|NCBI__GCF_000967895.1:WP_046011132.1 636 FADLKAKAEEIGDNLSCLMITYPSTHGVYEEGIKEICELVHSLGGQVYMDGANLNAQVGITQPAYLGAD 704
********************************************************************* PP
TIGR00461 684 vchlnlhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpis 752
v+h+nlhktf+iphGGGGpgmgpigv +hl pf+ + + v ++ esk +gavs+apyGsasil+is
lcl|NCBI__GCF_000967895.1:WP_046011132.1 705 VSHMNLHKTFAIPHGGGGPGMGPIGVAAHLEPFVAN---HAVRPIDNESKGQGAVSSAPYGSASILTIS 770
************************************...556678999********************* PP
TIGR00461 753 ymyikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvak 821
+myi +mG +Gl+ka++ a+l+anylakrl ++y+il+ g+++ vaheci+dlr+lke++gi ++d+ak
lcl|NCBI__GCF_000967895.1:WP_046011132.1 771 WMYITLMGGKGLRKATQHALLKANYLAKRLGEHYPILYSGNKGLVAHECIIDLRPLKEQTGITEVDIAK 839
********************************************************************* PP
TIGR00461 822 rlldyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphsl 890
rl+dyGfhapt+sfpvaGt+m+epteses+ e+drf +ami+ik ei a+ +Ge+++e+n+lknaph
lcl|NCBI__GCF_000967895.1:WP_046011132.1 840 RLMDYGFHAPTMSFPVAGTFMIEPTESESKAEIDRFANAMISIKGEIMAIHNGELDAENNPLKNAPH-T 907
*******************************************************************.5 PP
TIGR00461 891 qslivaewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
+++++w pys++ aa+p l +kfwp+v+r+dd+yGdrnl+csc
lcl|NCBI__GCF_000967895.1:WP_046011132.1 908 AAVVTGDWDRPYSQQLAAFPTKNLGAHKFWPSVGRIDDVYGDRNLICSC 956
6899********************************************* PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (964 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: 12.69
//
[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