Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate WP_090448472.1 BLS63_RS24800 glycine dehydrogenase (aminomethyl-transferring)
Query= reanno::pseudo3_N2E3:AO353_03500
(950 letters)
>NCBI__GCF_900100495.1:WP_090448472.1
Length = 951
Score = 1638 bits (4241), Expect = 0.0
Identities = 813/945 (86%), Positives = 867/945 (91%), Gaps = 1/945 (0%)
Query: 6 LSTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEAEA 65
L+T NEFIARHIGPR D AML +LGFDSLEAL+ASVIPDSIKG+SVLG GLSEA+A
Sbjct: 4 LTTQNEFIARHIGPREADTAAMLKALGFDSLEALTASVIPDSIKGSSVLGQAPGLSEADA 63
Query: 66 LASIKAIAAKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEAL 125
LA +KAIA NQ FK+YIGQGYY HTPS ILRNLLENPAWYTAYTPYQPEISQGRLEAL
Sbjct: 64 LAKLKAIAGHNQQFKSYIGQGYYGTHTPSAILRNLLENPAWYTAYTPYQPEISQGRLEAL 123
Query: 126 LNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASIHSHPQTLDVL 185
LNFQTLI DLTGLPIANASLLDEATAAAEAMTFCKRLSKNK S AFFAS H HPQTLDVL
Sbjct: 124 LNFQTLIGDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKASQAFFASAHCHPQTLDVL 183
Query: 186 RTRAEPLGIDVVVGDERELTDVSAFFGALLQYPASNGDLFDYRELTERFHAVNALVAVAA 245
RTRAEPLGI+VVVGDERE+TD SA+FGALLQYPASNG++FDYR L ERFHA NALVAVAA
Sbjct: 184 RTRAEPLGIEVVVGDEREITDASAYFGALLQYPASNGEIFDYRALVERFHAANALVAVAA 243
Query: 246 DLLALTVLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVD 305
DLLAL +LTPPGEFGAD+AIGSAQRFGVPLGFGGPHAAYF+T+D FKRDMPGRLVGVS+D
Sbjct: 244 DLLALCLLTPPGEFGADLAIGSAQRFGVPLGFGGPHAAYFATRDGFKRDMPGRLVGVSLD 303
Query: 306 RFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLKQIANRIHHL 365
RFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGP+GL +IA R+H L
Sbjct: 304 RFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPQGLTRIAKRVHQL 363
Query: 366 TAILAKGLSALGLNVEQANFFDTLTLATGANTAALHDKARAQRINLRVIDGERLGLSLDE 425
TAILA+GLS LGL VEQ +FFDT+TLA+GA TA LH +ARA INLR ID E LGLSLDE
Sbjct: 364 TAILAQGLSKLGLAVEQDSFFDTITLASGARTAQLHQQARAMGINLRQIDAEHLGLSLDE 423
Query: 426 TTTQADIETLWSVLAD-GKALPDFAALAASVQSRIPAELVRQSPILSHPVFNRYHSETEL 484
TT QA +E LW V A+ G +LP+FA LA V +R+P L+R S IL+HPVFNRYHSETEL
Sbjct: 424 TTDQAAVEALWEVFAEPGHSLPNFAELAGQVAARLPQALLRSSKILAHPVFNRYHSETEL 483
Query: 485 MRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPPAQSAGYQQL 544
MRYLRKLADKDLALDR+MIPLGSCTMKLNAASEMIPVTWAEFG LHPFAP QS GY+QL
Sbjct: 484 MRYLRKLADKDLALDRSMIPLGSCTMKLNAASEMIPVTWAEFGNLHPFAPAEQSQGYRQL 543
Query: 545 TDELEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGEERRDICLIPSSAHGTN 604
TDELEAMLCAATGYD ISLQPNAGSQGEYAGLLAIRAYH+SRG+E+RDICLIPSSAHGTN
Sbjct: 544 TDELEAMLCAATGYDGISLQPNAGSQGEYAGLLAIRAYHRSRGDEQRDICLIPSSAHGTN 603
Query: 605 PATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIREIC 664
PATA+MAGMRVVVTACDARGNVDI DL+AKA EH+E LAALMITYPSTHGVFEEGIREI
Sbjct: 604 PATASMAGMRVVVTACDARGNVDIADLKAKAEEHKERLAALMITYPSTHGVFEEGIREIA 663
Query: 665 GIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKS 724
I+HDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVK+
Sbjct: 664 QIVHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKA 723
Query: 725 HLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNANYIS 784
HL PFLPGHA+M+RK GAV AAPFGSASILPITWMYI MMGG GLKRASQ+AILNANYI+
Sbjct: 724 HLIPFLPGHASMQRKVGAVSAAPFGSASILPITWMYISMMGGEGLKRASQMAILNANYIA 783
Query: 785 RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAG 844
RRLEEHYPVLYTGSN LVAHECILDLRPLK++SGISVDDVAKRLIDFGFHAPTMSFPVAG
Sbjct: 784 RRLEEHYPVLYTGSNSLVAHECILDLRPLKETSGISVDDVAKRLIDFGFHAPTMSFPVAG 843
Query: 845 TLMIEPTESESKEELDRFCDAMICIREEIRAVENGTLDKDDNPLKNAPHTAAEIVGEWTH 904
TLMIEPTESESKEELDRFCDAMI IREEIRAVE G LDKDDNPLKNAPHTA E+VGEWTH
Sbjct: 844 TLMIEPTESESKEELDRFCDAMIAIREEIRAVERGDLDKDDNPLKNAPHTALELVGEWTH 903
Query: 905 PYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLICACPSIESY 949
YSRE AVYPVASL++GKYWPPVGRVDNVFGDRNL+CACPSIE+Y
Sbjct: 904 GYSRELAVYPVASLVDGKYWPPVGRVDNVFGDRNLVCACPSIEAY 948
Lambda K H
0.319 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: 2395
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: 950
Length of database: 951
Length adjustment: 44
Effective length of query: 906
Effective length of database: 907
Effective search space: 821742
Effective search space used: 821742
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_090448472.1 BLS63_RS24800 (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.20439.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 1515.7 0.0 0 1515.6 0.0 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090448472.1 BLS63_RS24800 glycine dehydrogen
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090448472.1 BLS63_RS24800 glycine dehydrogenase (aminomethyl-transferring)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1515.6 0.0 0 0 1 939 [] 13 942 .. 13 942 .. 0.99
Alignments for each domain:
== domain 1 score: 1515.6 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyi 69
rh+Gp ea+ mlk+lGfd+l+al+ ++p++i+ + l +e +ala+lk+ia +n+++ksyi
lcl|NCBI__GCF_900100495.1:WP_090448472.1 13 RHIGPREADTAAMLKALGFDSLEALTASVIPDSIKGSSVLGQAPGLSEADALAKLKAIAGHNQQFKSYI 81
9**********************************999998888889********************** PP
TIGR00461 70 GkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaa 138
G+Gyy+t +p i+rnllenp wytaytpyqpeisqGrleallnfqt++ dltGl++anasllde+taa
lcl|NCBI__GCF_900100495.1:WP_090448472.1 82 GQGYYGTHTPSAILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLIGDLTGLPIANASLLDEATAA 150
********************************************************************* PP
TIGR00461 139 aeamalsfrvskkk.ankfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatd 206
aeam +++r+sk+k +++f+ + ++hpqtl+v++traeplgiev+v+d +++++a +G+llqypa++
lcl|NCBI__GCF_900100495.1:WP_090448472.1 151 AEAMTFCKRLSKNKaSQAFFASAHCHPQTLDVLRTRAEPLGIEVVVGDEREITDASAYFGALLQYPASN 219
**************667899999********************************************** PP
TIGR00461 207 GeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkde 275
Gei+dy+al+++ + +alv+vaadllal lltppg++Gad+++GsaqrfGvplG+GGphaa+fa++d
lcl|NCBI__GCF_900100495.1:WP_090448472.1 220 GEIFDYRALVERFHAANALVAVAADLLALCLLTPPGEFGADLAIGSAQRFGVPLGFGGPHAAYFATRDG 288
********************************************************************* PP
TIGR00461 276 ykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvllanvaslyavyhGpkGlknia 344
+kr +pGr+vGvs d+ G++alrla+qtreqhirr+katsnictaqvllan+as+yavyhGp+Gl +ia
lcl|NCBI__GCF_900100495.1:WP_090448472.1 289 FKRDMPGRLVGVSLDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPQGLTRIA 357
********************************************************************* PP
TIGR00461 345 rrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlkaaeeaeinlravvltevgialdett 413
+r+++lt+ila+gl + ++ ++++ +fdt+t+ g ++a ++ ++a++++inlr ++++++g++ldett
lcl|NCBI__GCF_900100495.1:WP_090448472.1 358 KRVHQLTAILAQGLSKLGLAVEQDSFFDTITLASGARTA-QLHQQARAMGINLRQIDAEHLGLSLDETT 425
*********************************999998.9**************************** PP
TIGR00461 414 tkedvldllkvlagkdnlgl.sseelsedvansfpaellrddeilrdevfnryhsetellrylhrlesk 481
++ v+ l++v+a ++l + el +va +p++llr+++il ++vfnryhsetel+ryl +l k
lcl|NCBI__GCF_900100495.1:WP_090448472.1 426 DQAAVEALWEVFAEPG-HSLpNFAELAGQVAARLPQALLRSSKILAHPVFNRYHSETELMRYLRKLADK 493
************9966.55527899******************************************** PP
TIGR00461 482 dlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaisl 550
dlal++smiplGsctmklna+ em+p+tw ef+++hpfapaeq++Gy++l +le+ l+ tG+d+isl
lcl|NCBI__GCF_900100495.1:WP_090448472.1 494 DLALDRSMIPLGSCTMKLNAASEMIPVTWAEFGNLHPFAPAEQSQGYRQLTDELEAMLCAATGYDGISL 562
********************************************************************* PP
TIGR00461 551 qpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlk 619
qpn+G+qGeyaGl +ir yh srg+e+r+iclip sahGtnpa+a maG++vv+ +cd Gn+d+ dlk
lcl|NCBI__GCF_900100495.1:WP_090448472.1 563 QPNAGSQGEYAGLLAIRAYHRSRGDEQRDICLIPSSAHGTNPATASMAGMRVVVTACDARGNVDIADLK 631
********************************************************************* PP
TIGR00461 620 akaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchln 688
akae++ ++laa+m+typst+Gvfee+ire+ +ivh GGqvy+dGanmna vGl++pg++G dv+hln
lcl|NCBI__GCF_900100495.1:WP_090448472.1 632 AKAEEHKERLAALMITYPSTHGVFEEGIREIAQIVHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLN 700
********************************************************************* PP
TIGR00461 689 lhktfsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyik 757
lhktf+iphGGGGpg+gpigvk+hl+pflp+ ++++++gavsaap+Gsasilpi++myi
lcl|NCBI__GCF_900100495.1:WP_090448472.1 701 LHKTFCIPHGGGGPGVGPIGVKAHLIPFLPG--------HASMQRKVGAVSAAPFGSASILPITWMYIS 761
*******************************........4578899*********************** PP
TIGR00461 758 mmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldy 826
mmG eGlk+as++ailnany+a+rl+++y++l++g++ vahecildlr+lke +gi++ dvakrl+d+
lcl|NCBI__GCF_900100495.1:WP_090448472.1 762 MMGGEGLKRASQMAILNANYIARRLEEHYPVLYTGSNSLVAHECILDLRPLKETSGISVDDVAKRLIDF 830
********************************************************************* PP
TIGR00461 827 GfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqsliv 895
Gfhapt+sfpvaGtlm+epteses+eeldrf+damiai+eei av G+++++dn+lknaph++ ++v
lcl|NCBI__GCF_900100495.1:WP_090448472.1 831 GFHAPTMSFPVAGTLMIEPTESESKEELDRFCDAMIAIREEIRAVERGDLDKDDNPLKNAPHTA-LELV 898
**************************************************************65.6789 PP
TIGR00461 896 aewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
+ew++ ysre a+yp++ l k+wp v+r+d+++Gdrnlvc+c
lcl|NCBI__GCF_900100495.1:WP_090448472.1 899 GEWTHGYSRELAVYPVASLVDGKYWPPVGRVDNVFGDRNLVCAC 942
******************999**********************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (951 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: 8.82
//
[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