Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate 3609294 Dshi_2680 glycine dehydrogenase (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
(950 letters)
>FitnessBrowser__Dino:3609294
Length = 954
Score = 1153 bits (2983), Expect = 0.0
Identities = 570/940 (60%), Positives = 697/940 (74%), Gaps = 10/940 (1%)
Query: 15 RHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEADALALIKSIAT 74
RHIGP + ML +LG SLEAL +P+ I+ L LSE D L ++ +A
Sbjct: 17 RHIGPSPKEMGQMLATLGVPSLEALINEALPEGIRRRDPLAFGPALSERDTLHRMRELAD 76
Query: 75 KNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISD 134
KN + + IGQGY+GTHTP ILRN+LENPAWYTAYTPYQPEISQGRLEALLNFQT+++D
Sbjct: 77 KNTVLTSLIGQGYHGTHTPPVILRNILENPAWYTAYTPYQPEISQGRLEALLNFQTMMAD 136
Query: 135 LTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQTLDVLRTRAEPLGI 194
LTGLPIANASLLDE TAAAEAM +R SK+K + FF + CHPQT+DV+RTRAEPLGI
Sbjct: 137 LTGLPIANASLLDEGTAAAEAMAMAQRASKSK-ARGFFVAEDCHPQTIDVIRTRAEPLGI 195
Query: 195 DVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANALVAVAADLLALTVLT 254
+V+VG L D F AL QYP S G V DY ++ E H A AL VAAD LALT+L
Sbjct: 196 EVIVGAVDAL-DPEAVFAALFQYPGSYGHVRDYSDVIEALHGARALAVVAADPLALTLLK 254
Query: 255 APGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGNPALRL 314
+PGE GAD+AIGS QRFGVP+G+GGPHAAY + DA KR MPGR++GVSVD GN A RL
Sbjct: 255 SPGEMGADIAIGSTQRFGVPMGYGGPHAAYMTCTDALKRSMPGRIIGVSVDARGNKAYRL 314
Query: 315 AMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIANRVHHLTAILAKGLS 374
++QTREQHIRREKA SN+CTAQ LLA +ASMY V+HGP GL IA VH TA +A GL+
Sbjct: 315 SLQTREQHIRREKANSNVCTAQALLAVMASMYGVFHGPDGLKAIAQTVHRKTARMADGLT 374
Query: 375 ALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLGLSLDETTTQADVET 434
LG V+ +FDT+TVK G+ + A + +NLR V +R+G++LDE T +E
Sbjct: 375 ELGFKVDPQDYFDTITVKVGSMQGVILAAALREGVNLRKVGTDRIGITLDELTLGRTIEA 434
Query: 435 LWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHSETELMRYLRKLADK 494
+W + D + +P ++R+S ++HP+F+ +E E+ RY+R+LAD+
Sbjct: 435 VWRAFGAEGMVYDKTRMVYH----LPQEMLRESSYMTHPIFHMNRAEAEMTRYMRRLADR 490
Query: 495 DLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYQQLTDELEAMLCA 554
DLALDR MIPLGSCTMKLNA EM+P+TW EF LHPFAPA+Q+AGY ++ EL MLC
Sbjct: 491 DLALDRAMIPLGSCTMKLNATVEMLPLTWPEFANLHPFAPADQAAGYHEMIAELSQMLCD 550
Query: 555 ATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSAHGTNPATAQMAGMR 614
TGYD++S+QPN+G+QGEYAGLLAIR YH++RGE R+ICLIP+SAHGTNPA+AQM G +
Sbjct: 551 VTGYDAMSMQPNSGAQGEYAGLLAIRGYHRARGEGHRNICLIPTSAHGTNPASAQMVGWK 610
Query: 615 VVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIREICGIIHDNGGQV 674
VVV G++D+ED RAKA +H E+LA MITYPSTHGVFEE +RE+C I H +GGQV
Sbjct: 611 VVVVKSAENGDIDLEDFRAKAEQHSENLAGCMITYPSTHGVFEEIVREVCDITHAHGGQV 670
Query: 675 YIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLAPFLPGHA 734
YIDGANMNAMVGL APG GGDVSHLNLHKTFCIPHGGGGPG+GPIGVK+HLAP LP HA
Sbjct: 671 YIDGANMNAMVGLSAPGDLGGDVSHLNLHKTFCIPHGGGGPGMGPIGVKAHLAPHLPSHA 730
Query: 735 QME----RKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNANYISRRLEEH 790
GAV +A +GS SIL I++ Y +MGGAGL +A+++AILNANY+++RL
Sbjct: 731 TATGAGFGDAGAVASAAYGSPSILTISYAYCLLMGGAGLTQATKVAILNANYMAKRLSAG 790
Query: 791 YPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGTLMIEP 850
+P+LY G VAHECILD R L +G++V+DVAKRL+D GFHAPTMS+PVAGTLM+EP
Sbjct: 791 FPILYANDKGRVAHECILDTRVLDKIAGVTVEDVAKRLMDCGFHAPTMSWPVAGTLMVEP 850
Query: 851 TESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVGEWSHPYSREQ 910
TESE K ELDRFCDAM+ IREE A+ G+LD ++NPLK APHT ++LVG+W PYSREQ
Sbjct: 851 TESEPKAELDRFCDAMLAIREEADAIAAGSLDAENNPLKRAPHTVEDLVGDWDRPYSREQ 910
Query: 911 AVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 950
A YP + KYWPPV RVDN +GDRNLVC CP +E YA
Sbjct: 911 ACYPPGAFRVDKYWPPVNRVDNAYGDRNLVCTCPPVEDYA 950
Lambda K H
0.319 0.135 0.398
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: 2257
Number of extensions: 91
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: 950
Length of database: 954
Length adjustment: 44
Effective length of query: 906
Effective length of database: 910
Effective search space: 824460
Effective search space used: 824460
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 3609294 Dshi_2680 (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.15784.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 1418.8 0.0 0 1418.6 0.0 1.0 1 lcl|FitnessBrowser__Dino:3609294 Dshi_2680 glycine dehydrogenase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609294 Dshi_2680 glycine dehydrogenase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1418.6 0.0 0 0 1 939 [] 17 943 .. 17 943 .. 0.98
Alignments for each domain:
== domain 1 score: 1418.6 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyati 77
rh+Gp++ e+ +ml tlG+ +l+ali++++p+ ir + pl ++ + +e ++l +++++a+kn +++s iG+Gy +t
lcl|FitnessBrowser__Dino:3609294 17 RHIGPSPKEMGQMLATLGVPSLEALINEALPEGIRRRDPLAFGPALSERDTLHRMRELADKNTVLTSLIGQGYHGTH 93
9**************************************************************************** PP
TIGR00461 78 lppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkkan 154
+ppvi+rn+lenp wytaytpyqpeisqGrleallnfqt++ dltGl++anaslldegtaaaeama+++r sk+ka
lcl|FitnessBrowser__Dino:3609294 94 TPPVILRNILENPAWYTAYTPYQPEISQGRLEALLNFQTMMADLTGLPIANASLLDEGTAAAEAMAMAQRASKSKAR 170
***************************************************************************** PP
TIGR00461 155 kfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaad 231
f+va+d+hpqt++v++traeplgieviv+ ++ + v+ +l qyp++ G++ dy ++i++l+ +al vaad
lcl|FitnessBrowser__Dino:3609294 171 GFFVAEDCHPQTIDVIRTRAEPLGIEVIVGAVD-ALDPEAVFAALFQYPGSYGHVRDYSDVIEALHGARALAVVAAD 246
****************************99765.567889************************************* PP
TIGR00461 232 llaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhi 308
+laltll++pg++Gadi++Gs+qrfGvp+GyGGphaa++++ d +kr++pGri+Gvs da Gn a rl+lqtreqhi
lcl|FitnessBrowser__Dino:3609294 247 PLALTLLKSPGEMGADIAIGSTQRFGVPMGYGGPHAAYMTCTDALKRSMPGRIIGVSVDARGNKAYRLSLQTREQHI 323
***************************************************************************** PP
TIGR00461 309 rrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaase 385
rr+ka+sn+ctaq+lla++as+y+v+hGp Glk ia+ ++r t+ +a gl + ++++ + yfdt+tv+vg +
lcl|FitnessBrowser__Dino:3609294 324 RREKANSNVCTAQALLAVMASMYGVFHGPDGLKAIAQTVHRKTARMADGLTELGFKVDPQDYFDTITVKVGSMQG-V 399
***********************************************************************9999.7 PP
TIGR00461 386 vlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpaellrddeilrdevf 462
+l aa ++nlr v ++ +gi+lde t + ++ +++ + ++ + +++ + +p+e+lr++ ++++++f
lcl|FitnessBrowser__Dino:3609294 400 ILAAALREGVNLRKVGTDRIGITLDELTLGRTIEAVWRAFGAEG-MVYDKT----RMVYHLPQEMLRESSYMTHPIF 471
88899999********************************9954.444433....344579**************** PP
TIGR00461 463 nryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwl 539
++ +e+e+ ry+ rl +dlal+++miplGsctmklnat+emlp+twpefa++hpfapa+q+ Gy+e+ia+l + l
lcl|FitnessBrowser__Dino:3609294 472 HMNRAEAEMTRYMRRLADRDLALDRAMIPLGSCTMKLNATVEMLPLTWPEFANLHPFAPADQAAGYHEMIAELSQML 548
***************************************************************************** PP
TIGR00461 540 veitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlv 616
+++tG+da+s+qpnsGaqGeyaGl +ir yh +rge+hrniclip+sahGtnpasa+m+G kvv+vk ++G+idl+
lcl|FitnessBrowser__Dino:3609294 549 CDVTGYDAMSMQPNSGAQGEYAGLLAIRGYHRARGEGHRNICLIPTSAHGTNPASAQMVGWKVVVVKSAENGDIDLE 625
***************************************************************************** PP
TIGR00461 617 dlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktf 693
d++akae+++++la m+typst+Gvfee +rev+di h GGqvy+dGanmna vGl++pgdlG dv+hlnlhktf
lcl|FitnessBrowser__Dino:3609294 626 DFRAKAEQHSENLAGCMITYPSTHGVFEEIVREVCDITHAHGGQVYIDGANMNAMVGLSAPGDLGGDVSHLNLHKTF 702
***************************************************************************** PP
TIGR00461 694 siphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasev 770
+iphGGGGpgmgpigvk+hlap+lp + ++++ g gav++a yGs sil+isy+y +mG Gl++a++v
lcl|FitnessBrowser__Dino:3609294 703 CIPHGGGGPGMGPIGVKAHLAPHLPS---HATATGAGF-GDAGAVASAAYGSPSILTISYAYCLLMGGAGLTQATKV 775
**************************...667776655.5689********************************** PP
TIGR00461 771 ailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmvepte 847
ailnany+akrl ++il+ + ++rvahecild r l + ag+ ++dvakrl+d Gfhapt+s+pvaGtlmvepte
lcl|FitnessBrowser__Dino:3609294 776 AILNANYMAKRLSAGFPILYANDKGRVAHECILDTRVLDKIAGVTVEDVAKRLMDCGFHAPTMSWPVAGTLMVEPTE 852
***************************************************************************** PP
TIGR00461 848 sesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaaypapvlkyfkfwptva 924
se + eldrf+dam+ai+ee+da+ aG +++e+n+lk aph++++l v++w pysre+a+yp + + k+wp v+
lcl|FitnessBrowser__Dino:3609294 853 SEPKAELDRFCDAMLAIREEADAIAAGSLDAENNPLKRAPHTVEDL-VGDWDRPYSREQACYPPGAFRVDKYWPPVN 928
*****************************************99985.79**************************** PP
TIGR00461 925 rlddtyGdrnlvcsc 939
r+d++yGdrnlvc+c
lcl|FitnessBrowser__Dino:3609294 929 RVDNAYGDRNLVCTC 943
**************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (954 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 0.02s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 12.53
//
[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