Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate 199967 SO0781 glycine cleavage system P protein (NCBI ptt file)
Query= reanno::Koxy:BWI76_RS23870
(957 letters)
>FitnessBrowser__MR1:199967
Length = 962
Score = 1350 bits (3494), Expect = 0.0
Identities = 661/960 (68%), Positives = 796/960 (82%), Gaps = 6/960 (0%)
Query: 3 QTLGQLENRDAFIERHIGPDALQQQEMLKTVGADSLNALIGQIVPQDIQLATPPQVGEAT 62
QTL QLE D F+ RHIGPD+ QQQEML VGA+SL+ L QIVP+ I+L+ +G++
Sbjct: 4 QTLTQLEQHDLFLRRHIGPDSSQQQEMLNYVGAESLDDLTAQIVPESIRLSQELSIGDSC 63
Query: 63 TEFAALAELKAIAGRNKRFKSYIGMGYTAVQLPPVIQRNMLENPGWYTAYTPYQPEVSQG 122
E +A ++ +A +N+ FKSYIGMGY Q+P VI RN+LENPGWYTAYTPYQPE++QG
Sbjct: 64 GEAEGIAYIRGLAKQNQVFKSYIGMGYYGTQVPNVILRNVLENPGWYTAYTPYQPEIAQG 123
Query: 123 RLESLLNFQQVTLDLTGLDIASASLLDEATAAAEAMAMAKRVSKLKNANRFFVAADVHPQ 182
RLE++LNFQQV++DLTGLD+ASASLLDEATAAAEAMA+AKRVSK K AN FFVA DV PQ
Sbjct: 124 RLEAILNFQQVSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKKANIFFVADDVFPQ 183
Query: 183 TLDVVRTRAETFGFDVIVDDAEKALDHQDVFGVLLQQVGTTGEVHDYSKLIADLKARKVI 242
TLDVV+TRAE FGF+V+V A +A++H+ +FG L Q G++ D++ L A+L+A+ VI
Sbjct: 184 TLDVVKTRAECFGFEVVVGPASEAVNHE-LFGALFQYSNRFGQITDFTDLFAELRAKNVI 242
Query: 243 VSVAADFMALVLLTAPGKQGADIVFGSAQRFGVPMGYGGPHAAFFAAKDEFKRSMPGRII 302
V+VAAD M+LVLL +PG GAD+VFGSAQRFGVPMG+GGPHAAFF A+DE KRSMPGRII
Sbjct: 243 VTVAADIMSLVLLKSPGSMGADVVFGSAQRFGVPMGFGGPHAAFFVARDEHKRSMPGRII 302
Query: 303 GVSKDAAGNTALRMAMQTREQHIRREKANSNICTSQVLLANIASLYAVFHGPAGLKRIAS 362
GVSKD GN ALRMAMQTREQHIRREKANSNICT+Q+LLAN+AS YAVFHGP GLK IAS
Sbjct: 303 GVSKDTRGNRALRMAMQTREQHIRREKANSNICTAQILLANMASFYAVFHGPQGLKTIAS 362
Query: 363 RIHRLTDILADGLQKKGLKLRHAHYFDTLCVEVADKAAVLARAEALRINLRSDIHHAVGI 422
RI+R DILA GLQ KG+ L + +FDT+ ++ D AAV ARA A +NLR D VG+
Sbjct: 363 RINRFADILAAGLQAKGVSLVNNTWFDTISIKGLDVAAVNARALAAEMNLRFDADGIVGV 422
Query: 423 TLDEATTREDVLNLFRAILGDDHGLDIDTLDKD-VALDSRSIPASMLRDDAILTHPVFNR 481
+LDE T R D+ LF ILG HGLD+ LD VA S+SIPAS++R+DAIL+HP FNR
Sbjct: 423 SLDETTIRTDIDALFEVILGAGHGLDVAALDAQIVAQGSQSIPASLVREDAILSHPTFNR 482
Query: 482 YHSETEMMRYMHALERKDLALNQAMIPLGSCTMKLNAAAEMIPITWPEFAELHPFCPVDQ 541
Y SETEMMRY+ LE KDLALN +MI LGSCTMKLNAA EMIP++WPEFA +HPFCP+DQ
Sbjct: 483 YQSETEMMRYIKRLESKDLALNYSMISLGSCTMKLNAAVEMIPVSWPEFANMHPFCPLDQ 542
Query: 542 AEGYHQMIAQLSDWLVKLTGYDAVCMQPNSGAQGEYAGLLAIRHYHESRNEGHRDICLIP 601
A+GY Q+I +LS WLV +TGYDAVC+QPNSGAQGEYAGLLAIR YHESR E HR+ICLIP
Sbjct: 543 AKGYTQLIEELSSWLVNVTGYDAVCIQPNSGAQGEYAGLLAIRKYHESRGEAHRNICLIP 602
Query: 602 SSAHGTNPASAQMAGMQVVVVACDKNGNIDLADLRAKAEQHAANLSCIMVTYPSTHGVYE 661
SAHGTNPASAQ+AGMQVVV ACDK GN+DL DL+AKA + A NLSCIM+TYPSTHGVYE
Sbjct: 603 QSAHGTNPASAQLAGMQVVVTACDKQGNVDLEDLKAKAAEVAENLSCIMITYPSTHGVYE 662
Query: 662 ETIREVCEVVHQFGGQVYLDGANMNAQVGITSPGFIGADVSHLNLHKTFCIPHGGGGPGM 721
ET+RE+C +VHQ GGQVYLDGANMNAQVG+TSPGFIGADVSHLNLHKTF IPHGGGGPGM
Sbjct: 663 ETVREICNIVHQHGGQVYLDGANMNAQVGLTSPGFIGADVSHLNLHKTFAIPHGGGGPGM 722
Query: 722 GPIGVKSHLAQFVPGHSVVQIEGMLTRQGAVSAAPFGSASILPISWMYIRMMGAEGLKQA 781
GPIGVK+HLA FV GH VV+ GAVSAAP+GSA ILPISWMYI+++G++GLK++
Sbjct: 723 GPIGVKAHLAPFVAGHVVVKPGRESDNNGAVSAAPYGSAGILPISWMYIKLLGSKGLKKS 782
Query: 782 SQMAILNANYIATRLKDAFPVLYTGRDGRVAHECILDIRPLKEETGISELDIAKRLIDFG 841
+Q A+LNANY+ +L + +PVL+ GR+ RVAHECI+D+RP+KE +G++E+DIAKRL D+G
Sbjct: 783 TQTALLNANYVMKKLSEHYPVLFRGRNDRVAHECIIDLRPIKEASGVTEMDIAKRLNDYG 842
Query: 842 FHAPTMSFPVAGTLMVEPTESESKVELDRFIDAMLAIRGEIDRVKAGEWPLEDNPLVNAP 901
FHAPTMSFPVAGTLM+EPTESESKVELDRFIDAM++IR EI +V+AGEWP ++NPL NAP
Sbjct: 843 FHAPTMSFPVAGTLMIEPTESESKVELDRFIDAMVSIRAEIAKVEAGEWPADNNPLHNAP 902
Query: 902 HTQGELVSAW--NHPYARELAVFPAGL--NNKYWPTVKRLDDVYGDRNLFCSCVPMSEYQ 957
HT +++ + + PY+RE+AVFP+ NK+WPTV R+DDVYGDRNLFC+CVP+S+Y+
Sbjct: 903 HTMADIMDSAFDSRPYSREVAVFPSAAVRTNKFWPTVNRIDDVYGDRNLFCACVPLSDYE 962
Lambda K H
0.320 0.135 0.399
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: 2233
Number of extensions: 75
Number of successful extensions: 6
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 199967 SO0781 (glycine cleavage system P protein (NCBI ptt file))
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.27566.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 1534.2 0.1 0 1534.0 0.1 1.0 1 lcl|FitnessBrowser__MR1:199967 SO0781 glycine cleavage system P
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199967 SO0781 glycine cleavage system P protein (NCBI ptt file)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1534.0 0.1 0 0 1 939 [] 18 955 .. 18 955 .. 0.98
Alignments for each domain:
== domain 1 score: 1534.0 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyatilp 79
rh+Gpd+++q++ml+ +G+++l++l+ q+vp++irl++ l ++ + e e +a ++ +a++n+++ksyiG+Gyy+t++p
lcl|FitnessBrowser__MR1:199967 18 RHIGPDSSQQQEMLNYVGAESLDDLTAQIVPESIRLSQELSIGDSCGEAEGIAYIRGLAKQNQVFKSYIGMGYYGTQVP 96
9****************************************************************************** PP
TIGR00461 80 pviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkk.ankfv 157
vi+rn+lenpgwytaytpyqpei+qGrlea+lnfq+v +dltGl++a+asllde+taaaeamal++rvsk k an f+
lcl|FitnessBrowser__MR1:199967 97 NVILRNVLENPGWYTAYTPYQPEIAQGRLEAILNFQQVSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKkANIFF 175
***********************************************************************88799*** PP
TIGR00461 158 vakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaadllalt 236
va+dv pqtl+vvktrae +g+ev+v+ as+ ++ +++G+l qy+ G+i d+++l el+ ++++v+vaad+++l+
lcl|FitnessBrowser__MR1:199967 176 VADDVFPQTLDVVKTRAECFGFEVVVGPASEAVNH-ELFGALFQYSNRFGQITDFTDLFAELRAKNVIVTVAADIMSLV 253
*****************************998765.89***************************************** PP
TIGR00461 237 lltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkats 315
ll++pg +Gad+v+GsaqrfGvp+G+GGphaaff ++de+kr++pGri+Gvskd+ Gn alr+a+qtreqhirr+ka+s
lcl|FitnessBrowser__MR1:199967 254 LLKSPGSMGADVVFGSAQRFGVPMGFGGPHAAFFVARDEHKRSMPGRIIGVSKDTRGNRALRMAMQTREQHIRREKANS 332
******************************************************************************* PP
TIGR00461 316 nictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeae 394
nictaq+llan+as yav+hGp+Glk ia ri r+++ilaagl+ k+ +l n+t+fdt++++ + aa v+ +a +ae
lcl|FitnessBrowser__MR1:199967 333 NICTAQILLANMASFYAVFHGPQGLKTIASRINRFADILAAGLQAKGVSLVNNTWFDTISIKGLDVAA--VNARALAAE 409
**************************************************************998888..9******** PP
TIGR00461 395 inlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvan....sfpaellrddeilrdevfnryhset 469
+nlr + + vg++ldett + d+ l++v++g +gl++ l+ ++ s+pa l r+d il ++ fnry set
lcl|FitnessBrowser__MR1:199967 410 MNLRFDADGIVGVSLDETTIRTDIDALFEVILG-AGHGLDVAALDAQIVAqgsqSIPASLVREDAILSHPTFNRYQSET 487
*********************************.55*******99987544666************************* PP
TIGR00461 470 ellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdai 548
e++ry++rleskdlaln smi lGsctmklna++em+p++wpefa++hpf+p +q++Gy +li +l +wlv++tG+da+
lcl|FitnessBrowser__MR1:199967 488 EMMRYIKRLESKDLALNYSMISLGSCTMKLNAAVEMIPVSWPEFANMHPFCPLDQAKGYTQLIEELSSWLVNVTGYDAV 566
******************************************************************************* PP
TIGR00461 549 slqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagd 627
++qpnsGaqGeyaGl +ir+yhesrge hrniclip+sahGtnpasa++aG++vv+ +cdk+Gn+dl+dlkaka + ++
lcl|FitnessBrowser__MR1:199967 567 CIQPNSGAQGEYAGLLAIRKYHESRGEAHRNICLIPQSAHGTNPASAQLAGMQVVVTACDKQGNVDLEDLKAKAAEVAE 645
******************************************************************************* PP
TIGR00461 628 elaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgp 706
+l+++m+typst+Gv+eet+re+++ivh+ GGqvyldGanmnaqvGltspg++Gadv+hlnlhktf+iphGGGGpgmgp
lcl|FitnessBrowser__MR1:199967 646 NLSCIMITYPSTHGVYEETVREICNIVHQHGGQVYLDGANMNAQVGLTSPGFIGADVSHLNLHKTFAIPHGGGGPGMGP 724
******************************************************************************* PP
TIGR00461 707 igvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanylakrlkda 785
igvk+hlapf+ + + vv+ es + gavsaapyGsa ilpis+myik++G++Glkk+++ a+lnany++k+l ++
lcl|FitnessBrowser__MR1:199967 725 IGVKAHLAPFVAG---HVVVKPGRESDNNGAVSAAPYGSAGILPISWMYIKLLGSKGLKKSTQTALLNANYVMKKLSEH 800
*************...67788889999**************************************************** PP
TIGR00461 786 ykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmveptesesleeldrfidamiai 864
y++lf+gr++rvaheci+dlr++ke +g+ ++d+akrl dyGfhapt+sfpvaGtlm+epteses++eldrfidam++i
lcl|FitnessBrowser__MR1:199967 801 YPVLFRGRNDRVAHECIIDLRPIKEASGVTEMDIAKRLNDYGFHAPTMSFPVAGTLMIEPTESESKVELDRFIDAMVSI 879
******************************************************************************* PP
TIGR00461 865 keeidavkaGeiklednilknaphslqslivaewa.dpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
++ei +v aGe+++++n+l+naph++ + + + + pysre+a++p + ++ +kfwptv+r+dd+yGdrnl+c+c
lcl|FitnessBrowser__MR1:199967 880 RAEIAKVEAGEWPADNNPLHNAPHTMADIMDSAFDsRPYSREVAVFPSAAVRTNKFWPTVNRIDDVYGDRNLFCAC 955
****************************9988875157*************************************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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 11.58
//
[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