Align glycine dehydrogenase [decarboxylating]; EC 1.4.4.2 (characterized)
to candidate 5210634 Shew_3062 glycine dehydrogenase (RefSeq)
Query= CharProtDB::CH_003480
(957 letters)
>FitnessBrowser__PV4:5210634
Length = 962
Score = 1325 bits (3430), Expect = 0.0
Identities = 643/961 (66%), Positives = 787/961 (81%), Gaps = 6/961 (0%)
Query: 2 TQTLSQLENSGAFIERHIGPDAAQQQEMLNAVGAQSLNALTGQIVPKDIQLATPPQVGAP 61
T+TL+QLE FI RHIGPD+A QQEMLN VGA+SL LT QIVP+ I+L VG+
Sbjct: 3 TETLTQLEQHELFIRRHIGPDSADQQEMLNFVGAESLEDLTQQIVPESIRLGRDLAVGSA 62
Query: 62 ATEYAALAELKAIASRNKRFTSYIGMGYTAVQLPPVILRNMLENPGWYTAYTPYQPEVSQ 121
E LA ++ A +NK F SYIGMGY +P VI RN+ ENPGWYTAYTPYQPE++Q
Sbjct: 63 CGEAEGLASIRKYADKNKVFKSYIGMGYYGTIVPSVIQRNVFENPGWYTAYTPYQPEIAQ 122
Query: 122 GRLEALLNFQQVTLDLTGLDMASASLLDEATAAAEAMAMAKRVSKLKNANRFFVASDVHP 181
GRLEA+LNFQQ+++DLTGLD+ASASLLDEATAAAEAMA+AKRVSK K AN FF+A DV P
Sbjct: 123 GRLEAILNFQQLSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKKANIFFIADDVFP 182
Query: 182 QTLDVVRTRAETFGFEVIVDDAQKVLDHQDVFGVLLQQVGTTGEIHDYTALISELKSRKI 241
QT+DVV+TRAE FGFE++V A + ++++ +FG L Q G+I D+T L + L+ +K
Sbjct: 183 QTIDVVKTRAECFGFEIVVGPASEAVNYE-LFGALFQYTNHYGQITDFTELFAALQEKKA 241
Query: 242 VVSVAADIMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEYKRSMPGRI 301
VV+VAADIM+LV L +PG GAD+VFGSAQRFGVPMG+GGPHAAFF +D++KRS+PGRI
Sbjct: 242 VVTVAADIMSLVSLKSPGSMGADVVFGSAQRFGVPMGFGGPHAAFFVTRDQHKRSLPGRI 301
Query: 302 IGVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVYHGPVGLKRIA 361
IGVS+D GN ALRMAMQTREQHIRREKANSNICT+QVLLAN+AS YAV+HGP GLK IA
Sbjct: 302 IGVSQDTRGNRALRMAMQTREQHIRREKANSNICTAQVLLANMASFYAVFHGPQGLKIIA 361
Query: 362 NRIHRLTDILAAGLQQKGLKLRHAHYFDTLCVEVADKAGVLTRAEAAEINLRSDILNAVG 421
+RIHRL DI AAGL+ KG++L + +FDT+ +VAD A RA A E+NLR D +G
Sbjct: 362 DRIHRLADIFAAGLKAKGVELVNNTWFDTVSFKVADSAAAQARAIAGEVNLRIDSDGILG 421
Query: 422 ITLDETTTRENVMQLFNVLLGDNHGLDIDTLDKDV-AHDSRSIQPAMLRDDEILTHPVFN 480
+ + ETTTRE+V QLF+++LG+ HGLD+ +D D+ A+ S SI ++R D IL HP FN
Sbjct: 422 VAMAETTTREDVAQLFDIVLGEGHGLDVAAIDADIIANGSNSIPAELVRQDAILEHPTFN 481
Query: 481 RYHSETEMMRYMHSLERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPPE 540
RYHSETEMMRY+ LE KDLALN +MI LGSCTMKLNAA EM+P++WPEF +HPFCP +
Sbjct: 482 RYHSETEMMRYIKRLENKDLALNHSMISLGSCTMKLNAATEMMPVSWPEFGNMHPFCPQD 541
Query: 541 QAEGYQQMIAQLADWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLI 600
QA+GY ++I +L++WLV +TGYDA+CMQPNSGA GEYAGLLAI+ YHESR EGHR++CLI
Sbjct: 542 QAQGYAELIEELSNWLVDITGYDAMCMQPNSGASGEYAGLLAIKKYHESRGEGHRNVCLI 601
Query: 601 PASAHGTNPASAHMAGMQVVVVACDKNGNIDLTDLRAKAEQAGDNLSCIMVTYPSTHGVY 660
P SAHGTNPASA +AGM++VV ACDK GN+D+ DL+AKA + +NLSCIMVTYPSTHGVY
Sbjct: 602 PQSAHGTNPASAQLAGMKIVVTACDKQGNVDMEDLKAKAAEVAENLSCIMVTYPSTHGVY 661
Query: 661 EETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPG 720
EETI E+CEV+HQ GGQVYLDGANMNAQVG+TSPG IGADVSHLNLHKTF IPHGGGGPG
Sbjct: 662 EETISEICEVIHQHGGQVYLDGANMNAQVGLTSPGSIGADVSHLNLHKTFAIPHGGGGPG 721
Query: 721 MGPIGVKAHLAPFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKK 780
MGPIGVKAHLAPFV GH+VV+ GAVSAAP+GSASILPI+WMYI+++G +GL++
Sbjct: 722 MGPIGVKAHLAPFVAGHAVVKHGRESDNNGAVSAAPYGSASILPITWMYIKLLGYQGLRQ 781
Query: 781 ASQVAILNANYIASRLQDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDY 840
++Q+A+LNANY+ +L +PVLYTGR+ RVAHECI+D+RPLKE +G++E+DIAKRL DY
Sbjct: 782 STQMALLNANYVMKKLSAHYPVLYTGRNDRVAHECIIDLRPLKEASGVTEMDIAKRLNDY 841
Query: 841 GFHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRAEIDQVKAGVWPLEDNPLVNA 900
GFHAPTMSFPVAGTLM+EPTESESK ELDRFI+AM+AIR EI +V+AG WP ++NPL NA
Sbjct: 842 GFHAPTMSFPVAGTLMIEPTESESKAELDRFIEAMVAIRGEIAKVEAGEWPADNNPLHNA 901
Query: 901 PHIQSELV-AEW-AHPYSREVAVFPAGV--ADKYWPTVKRLDDVYGDRNLFCSCVPISEY 956
PH ++++ +E+ + PYSRE AVFP A+K+WPTV R+DDVYGDRNL CSC PI +Y
Sbjct: 902 PHTMADIMDSEFDSRPYSRETAVFPTAAVKANKFWPTVNRIDDVYGDRNLMCSCAPIDDY 961
Query: 957 Q 957
+
Sbjct: 962 K 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: 2256
Number of extensions: 82
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: 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 5210634 Shew_3062 (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.1861336.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 1534.3 0.6 0 1534.1 0.6 1.0 1 lcl|FitnessBrowser__PV4:5210634 Shew_3062 glycine dehydrogenase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210634 Shew_3062 glycine dehydrogenase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1534.1 0.6 0 0 1 939 [] 18 955 .. 18 955 .. 0.98
Alignments for each domain:
== domain 1 score: 1534.1 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyatil 78
rh+Gpd+a+q++ml+ +G+++l++l++q+vp++irl r l ++++ e e la ++k a+knk++ksyiG+Gyy+ti+
lcl|FitnessBrowser__PV4:5210634 18 RHIGPDSADQQEMLNFVGAESLEDLTQQIVPESIRLGRDLAVGSACGEAEGLASIRKYADKNKVFKSYIGMGYYGTIV 95
9***************************************************************************** PP
TIGR00461 79 ppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk.ank 155
p viqrn++enpgwytaytpyqpei+qGrlea+lnfq++ +dltGl++a+asllde+taaaeamal++rvsk k an
lcl|FitnessBrowser__PV4:5210634 96 PSVIQRNVFENPGWYTAYTPYQPEIAQGRLEAILNFQQLSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKkANI 173
************************************************************************88799* PP
TIGR00461 156 fvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaadll 233
f++a+dv pqt++vvktrae +g+e++v+ as+ + +++G+l qy+ G+i d+++l +l+++ka+v+vaad++
lcl|FitnessBrowser__PV4:5210634 174 FFIADDVFPQTIDVVKTRAECFGFEIVVGPASEAV-NYELFGALFQYTNHYGQITDFTELFAALQEKKAVVTVAADIM 250
******************************99975.579*************************************** PP
TIGR00461 234 altlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrd 311
+l+ l++pg +Gad+v+GsaqrfGvp+G+GGphaaff ++d++kr+lpGri+Gvs+d+ Gn alr+a+qtreqhirr+
lcl|FitnessBrowser__PV4:5210634 251 SLVSLKSPGSMGADVVFGSAQRFGVPMGFGGPHAAFFVTRDQHKRSLPGRIIGVSQDTRGNRALRMAMQTREQHIRRE 328
****************************************************************************** PP
TIGR00461 312 katsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlka 389
ka+snictaqvllan+as yav+hGp+Glk ia ri+rl++i+aaglk k+ el n+t+fdt++ +v++ aa + +
lcl|FitnessBrowser__PV4:5210634 329 KANSNICTAQVLLANMASFYAVFHGPQGLKIIADRIHRLADIFAAGLKAKGVELVNNTWFDTVSFKVADSAA--AQAR 404
*********************************************************************999..6788 PP
TIGR00461 390 aeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan....sfpaellrddeilrdevfn 463
a + e+nlr + + +g+a+ ettt+edv +l+++++g+ +gl++ ++ d+ s+pael r+d il+++ fn
lcl|FitnessBrowser__PV4:5210634 405 AIAGEVNLRIDSDGILGVAMAETTTREDVAQLFDIVLGE-GHGLDVAAIDADIIAngsnSIPAELVRQDAILEHPTFN 481
8899**********************************5.5*******99998444555******************* PP
TIGR00461 464 ryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlve 541
ryhsete++ry++rle+kdlaln+smi lGsctmklna++em+p++wpef+++hpf+p +q++Gy eli +l +wlv+
lcl|FitnessBrowser__PV4:5210634 482 RYHSETEMMRYIKRLENKDLALNHSMISLGSCTMKLNAATEMMPVSWPEFGNMHPFCPQDQAQGYAELIEELSNWLVD 559
****************************************************************************** PP
TIGR00461 542 itGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlk 619
itG+da+++qpnsGa GeyaGl +i++yhesrge+hrn+clip+sahGtnpasa++aG+k+v+ +cdk+Gn+d++dlk
lcl|FitnessBrowser__PV4:5210634 560 ITGYDAMCMQPNSGASGEYAGLLAIKKYHESRGEGHRNVCLIPQSAHGTNPASAQLAGMKIVVTACDKQGNVDMEDLK 637
****************************************************************************** PP
TIGR00461 620 akaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiph 697
aka + +++l+++mvtypst+Gv+eeti e+++++h+ GGqvyldGanmnaqvGltspg +Gadv+hlnlhktf+iph
lcl|FitnessBrowser__PV4:5210634 638 AKAAEVAENLSCIMVTYPSTHGVYEETISEICEVIHQHGGQVYLDGANMNAQVGLTSPGSIGADVSHLNLHKTFAIPH 715
****************************************************************************** PP
TIGR00461 698 GGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailna 775
GGGGpgmgpigvk+hlapf+ + + vv+ es + gavsaapyGsasilpi++myik++G +Gl++++++a+lna
lcl|FitnessBrowser__PV4:5210634 716 GGGGPGMGPIGVKAHLAPFVAG---HAVVKHGRESDNNGAVSAAPYGSASILPITWMYIKLLGYQGLRQSTQMALLNA 790
**********************...7788999999******************************************* PP
TIGR00461 776 nylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmvepteseslee 853
ny++k+l +y++l++gr++rvaheci+dlr+lke +g+ ++d+akrl dyGfhapt+sfpvaGtlm+epteses+ e
lcl|FitnessBrowser__PV4:5210634 791 NYVMKKLSAHYPVLYTGRNDRVAHECIIDLRPLKEASGVTEMDIAKRLNDYGFHAPTMSFPVAGTLMIEPTESESKAE 868
****************************************************************************** PP
TIGR00461 854 ldrfidamiaikeeidavkaGeiklednilknaphslqslivaewad.pysreeaaypapvlkyfkfwptvarlddty 930
ldrfi+am+ai+ ei +v aGe+++++n+l+naph++ + + +e+ pysre a++p + +k +kfwptv+r+dd+y
lcl|FitnessBrowser__PV4:5210634 869 LDRFIEAMVAIRGEIAKVEAGEWPADNNPLHNAPHTMADIMDSEFDSrPYSRETAVFPTAAVKANKFWPTVNRIDDVY 946
********************************************96526***************************** PP
TIGR00461 931 Gdrnlvcsc 939
Gdrnl+csc
lcl|FitnessBrowser__PV4:5210634 947 GDRNLMCSC 955
********* 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 25.24
//
[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