Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate AO356_18170 AO356_18170 glycine dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5558
(953 letters)
>FitnessBrowser__pseudo5_N2C3_1:AO356_18170
Length = 949
Score = 1859 bits (4815), Expect = 0.0
Identities = 932/953 (97%), Positives = 944/953 (99%), Gaps = 4/953 (0%)
Query: 1 MTVNLGTANEFIARHIGPRASDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMGDGQS 60
MTVNLGTANEFIARHIGPR+SDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMGDGQS
Sbjct: 1 MTVNLGTANEFIARHIGPRSSDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMGDGQS 60
Query: 61 EADALASIKAIAAKNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGR 120
EADALASIKAIA+KNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGR
Sbjct: 61 EADALASIKAIASKNQLFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGR 120
Query: 121 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQT 180
LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQT
Sbjct: 121 LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSNAFFASVHSHPQT 180
Query: 181 LDVLRTRAEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFHTANALV 240
LDVLRTRAEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFH ANALV
Sbjct: 181 LDVLRTRAEPLGIDVVVGDERELSDVSGFFGALLQYPASNGDLFDYRELTERFHAANALV 240
Query: 241 AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG 300
AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG
Sbjct: 241 AVAADLLALTLLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVG 300
Query: 301 VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANR 360
VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANR
Sbjct: 301 VSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLVQIANR 360
Query: 361 IHHLTAILAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVDAERLGL 420
IHHLTAILAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVD +RLGL
Sbjct: 361 IHHLTAILAKGLGALGLSVEQESFFDTLTLRTGAQTAALHDKARAQRINLRVVDTQRLGL 420
Query: 421 SLDETTSQADVEALLRLIGNLMADGKAVPDFAALAASVQSHIPAELVRQSAILSHPVFNR 480
SLDETTSQADVEAL +L+ADGKA+PDFAALAA+VQS IPAELVRQSAILSHPVFNR
Sbjct: 421 SLDETTSQADVEALW----SLLADGKALPDFAALAATVQSRIPAELVRQSAILSHPVFNR 476
Query: 481 YHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQ 540
YHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQ
Sbjct: 477 YHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQ 536
Query: 541 SAGYQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIP 600
SAGYQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIP
Sbjct: 537 SAGYQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIP 596
Query: 601 SSAHGTNPATAHMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFE 660
SSAHGTNPATA+MAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFE
Sbjct: 597 SSAHGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFE 656
Query: 661 EGIREICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGV 720
EGIREICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGV
Sbjct: 657 EGIREICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGV 716
Query: 721 GPIGVKSHLAPFLPGHASMERKQGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAI 780
GPIGVKSHLAPFLPGHA+M RK+GAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAI
Sbjct: 717 GPIGVKSHLAPFLPGHANMARKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAI 776
Query: 781 LNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPT 840
LNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPT
Sbjct: 777 LNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPT 836
Query: 841 MSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTAAE 900
MSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTAAE
Sbjct: 837 MSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDNPLKNAPHTAAE 896
Query: 901 IVGEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPSIESYA 953
+VGEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPS+ESYA
Sbjct: 897 LVGEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCACPSLESYA 949
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: 2597
Number of extensions: 88
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: 953
Length of database: 949
Length adjustment: 44
Effective length of query: 909
Effective length of database: 905
Effective search space: 822645
Effective search space used: 822645
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 AO356_18170 AO356_18170 (glycine dehydrogenase)
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.11463.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 1502.6 0.0 0 1502.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 AO356_18170 glycine dehydrogenas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 AO356_18170 glycine dehydrogenase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1502.5 0.0 0 0 1 939 [] 14 942 .. 14 942 .. 0.99
Alignments for each domain:
== domain 1 score: 1502.5 bits; conditional E-value: 0
TIGR00461 1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknk 63
rh+Gp +++ + ml+ lG+d+l+al ++p++i+ + l ++ ++e +ala +k+iaskn+
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 14 RHIGPRSSDEQAMLERLGYDSLEALSASVIPESIKGTSVLDMGDGQSEADALASIKAIASKNQ 76
9************************************************************** PP
TIGR00461 64 kvksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlev 126
+k+yiG+Gyy+ +p i+rnllenp wytaytpyqpeisqGrleallnfqt+++dltGl++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 77 LFKTYIGQGYYNCHTPAPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISDLTGLPI 139
*************************************************************** PP
TIGR00461 127 anaslldegtaaaeamalsfrvskkk.ankfvvakdvhpqtlevvktraeplgievivddask 188
anasllde+taaaeam +++r+sk+k +n+f+ + + hpqtl+v++traeplgi+v+v+d ++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 140 ANASLLDEATAAAEAMTFCKRLSKNKgSNAFFASVHSHPQTLDVLRTRAEPLGIDVVVGDERE 202
**************************99*********************************** PP
TIGR00461 189 vkkavdvlGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlG 251
+++ +G+llqypa++G+++dy++l+++ + +alv+vaadllaltlltppg++Gad+++G
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 203 LSDVSGFFGALLQYPASNGDLFDYRELTERFHAANALVAVAADLLALTLLTPPGEFGADVAIG 265
*************************************************************** PP
TIGR00461 252 saqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkat 314
saqrfGvplG+GGphaa+f++kd +kr +pGr+vGvs d+ G++alrla+qtreqhirr+kat
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 266 SAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGKPALRLAMQTREQHIRREKAT 328
*************************************************************** PP
TIGR00461 315 snictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltve 377
snictaqvllan+as+yavyhGpkGl +ia+ri++lt+ila+gl +++++++ +fdtlt++
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 329 SNICTAQVLLANIASMYAVYHGPKGLVQIANRIHHLTAILAKGLGALGLSVEQESFFDTLTLR 391
*************************************************************** PP
TIGR00461 378 vgekaasevlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelse 440
g ++a ++ +a+++ inlr v+++ +g++ldett+++dv+ l+ +la + l+ + l
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 392 TGAQTA-ALHDKARAQRINLRVVDTQRLGLSLDETTSQADVEALWSLLADGKALP-DFAALAA 452
****99.899999**********************************99866454.8899*** PP
TIGR00461 441 dvansfpaellrddeilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnata 503
v++ +pael r++ il ++vfnryhsetel+ryl +l kdlal+++miplGsctmklna+
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 453 TVQSRIPAELVRQSAILSHPVFNRYHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAAS 515
*************************************************************** PP
TIGR00461 504 emlpitwpefaeihpfapaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvi 566
em+p+tw ef+ +hpfapaeq+ Gy++l +le+ l+ tG+da+slqpn+G+qGeyaGl +i
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 516 EMIPVTWAEFGALHPFAPAEQSAGYQQLTDELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAI 578
*************************************************************** PP
TIGR00461 567 rsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdel 629
r yh+srge++r+iclip sahGtnpa+a+maG++vv+ +cd Gn+d++dl+aka ++ ++l
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 579 RAYHQSRGEDRRDICLIPSSAHGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHL 641
*************************************************************** PP
TIGR00461 630 aavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhkt 692
aa+m+typst+Gvfee+ire++ i+h GGqvy+dGanmna vGl++pg++G dv+hlnlhkt
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 642 AALMITYPSTHGVFEEGIREICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKT 704
*************************************************************** PP
TIGR00461 693 fsiphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymy 755
f+iphGGGGpg+gpigvkshlapflp++ + ++ gav aap+Gsasilpi++my
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 705 FCIPHGGGGPGVGPIGVKSHLAPFLPGH--------ANMARKEGAVCAAPFGSASILPITWMY 759
***************************4........45778899******************* PP
TIGR00461 756 ikmmGaeGlkkasevailnanylakrlkdaykilfvgrdervahecildlrelkekagieald 818
i+mmG Glk+as++ailnany+a+rl+++y++l+ g+++ vahecildlr+lk+ +gi++ d
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 760 IRMMGGAGLKRASQLAILNANYIARRLEEHYPVLYSGSNGLVAHECILDLRPLKDSSGISVDD 822
*************************************************************** PP
TIGR00461 819 vakrlldyGfhaptlsfpvaGtlmveptesesleeldrfidamiaikeeidavkaGeikledn 881
vakrl+d+Gfhapt+sfpvaGtlm+epteses+eeldrf+dami+i+eei av +G ++++dn
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 823 VAKRLIDFGFHAPTMSFPVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGSLDKDDN 885
*************************************************************** PP
TIGR00461 882 ilknaphslqslivaewadpysreeaaypapvlkyfkfwptvarlddtyGdrnlvcsc 939
+lknaph+ ++v+ew++pysre+a+yp++ l k+wp v+r+d+++Gdrnlvc+c
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18170 886 PLKNAPHT-AAELVGEWTHPYSREQAVYPVASLIDGKYWPPVGRVDNVFGDRNLVCAC 942
*******6.56789*****************9999**********************9 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (939 nodes)
Target sequences: 1 (949 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 9.30
//
[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