GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Pseudomonas fluorescens FW300-N2E3

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate AO353_03500 AO353_03500 glycine dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_03500
         (950 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03500
          Length = 950

 Score = 1896 bits (4911), Expect = 0.0
 Identities = 950/950 (100%), Positives = 950/950 (100%)

Query: 1   MTQVNLSTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL 60
           MTQVNLSTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL
Sbjct: 1   MTQVNLSTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL 60

Query: 61  SEAEALASIKAIAAKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQG 120
           SEAEALASIKAIAAKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQG
Sbjct: 61  SEAEALASIKAIAAKNQLFKTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQG 120

Query: 121 RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASIHSHPQ 180
           RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASIHSHPQ
Sbjct: 121 RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASIHSHPQ 180

Query: 181 TLDVLRTRAEPLGIDVVVGDERELTDVSAFFGALLQYPASNGDLFDYRELTERFHAVNAL 240
           TLDVLRTRAEPLGIDVVVGDERELTDVSAFFGALLQYPASNGDLFDYRELTERFHAVNAL
Sbjct: 181 TLDVLRTRAEPLGIDVVVGDERELTDVSAFFGALLQYPASNGDLFDYRELTERFHAVNAL 240

Query: 241 VAVAADLLALTVLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV 300
           VAVAADLLALTVLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV
Sbjct: 241 VAVAADLLALTVLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV 300

Query: 301 GVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLKQIAN 360
           GVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLKQIAN
Sbjct: 301 GVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLKQIAN 360

Query: 361 RIHHLTAILAKGLSALGLNVEQANFFDTLTLATGANTAALHDKARAQRINLRVIDGERLG 420
           RIHHLTAILAKGLSALGLNVEQANFFDTLTLATGANTAALHDKARAQRINLRVIDGERLG
Sbjct: 361 RIHHLTAILAKGLSALGLNVEQANFFDTLTLATGANTAALHDKARAQRINLRVIDGERLG 420

Query: 421 LSLDETTTQADIETLWSVLADGKALPDFAALAASVQSRIPAELVRQSPILSHPVFNRYHS 480
           LSLDETTTQADIETLWSVLADGKALPDFAALAASVQSRIPAELVRQSPILSHPVFNRYHS
Sbjct: 421 LSLDETTTQADIETLWSVLADGKALPDFAALAASVQSRIPAELVRQSPILSHPVFNRYHS 480

Query: 481 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPPAQSAG 540
           ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPPAQSAG
Sbjct: 481 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPPAQSAG 540

Query: 541 YQQLTDELEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGEERRDICLIPSSA 600
           YQQLTDELEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGEERRDICLIPSSA
Sbjct: 541 YQQLTDELEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGEERRDICLIPSSA 600

Query: 601 HGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 660
           HGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI
Sbjct: 601 HGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 660

Query: 661 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 720
           REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI
Sbjct: 661 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 720

Query: 721 GVKSHLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA 780
           GVKSHLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA
Sbjct: 721 GVKSHLTPFLPGHAAMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA 780

Query: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840
           NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF
Sbjct: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840

Query: 841 PVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGTLDKDDNPLKNAPHTAAEIVG 900
           PVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGTLDKDDNPLKNAPHTAAEIVG
Sbjct: 841 PVAGTLMIEPTESESKEELDRFCDAMICIREEIRAVENGTLDKDDNPLKNAPHTAAEIVG 900

Query: 901 EWTHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLICACPSIESYA 950
           EWTHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLICACPSIESYA
Sbjct: 901 EWTHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLICACPSIESYA 950


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: 2591
Number of extensions: 92
Number of successful extensions: 3
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: 950
Length adjustment: 44
Effective length of query: 906
Effective length of database: 906
Effective search space:   820836
Effective search space used:   820836
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 AO353_03500 AO353_03500 (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.16901.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 1499.5   0.0          0 1499.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500  AO353_03500 glycine dehydrogenas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500  AO353_03500 glycine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1499.3   0.0         0         0       1     939 []      15     943 ..      15     943 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1499.3 bits;  conditional E-value: 0
                                     TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkv 65 
                                                   rh+Gp + + + ml++lGfd+l+al   ++p++i+ +  l le   +e eala +k+ia+kn+ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500  15 RHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEAEALASIKAIAAKNQLF 79 
                                                   9**************************************************************** PP

                                     TIGR00461  66 ksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanas 130
                                                   k+yiG+Gyy+  +p  i+rnllenp wytaytpyqpeisqGrleallnfqt+++dltGl++anas
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500  80 KTYIGQGYYNCHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISDLTGLPIANAS 144
                                                   ***************************************************************** PP

                                     TIGR00461 131 lldegtaaaeamalsfrvskkk.ankfvvakdvhpqtlevvktraeplgievivddaskvkkavd 194
                                                   llde+taaaeam +++r+sk+k + +f+ + + hpqtl+v++traeplgi+v+v+d +++++   
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 145 LLDEATAAAEAMTFCKRLSKNKgSHAFFASIHSHPQTLDVLRTRAEPLGIDVVVGDERELTDVSA 209
                                                   **********************8899*************************************** PP

                                     TIGR00461 195 vlGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvp 259
                                                    +G+llqypa++G+++dy++l+++ +  +alv+vaadllalt+ltppg++Gad+++GsaqrfGvp
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 210 FFGALLQYPASNGDLFDYRELTERFHAVNALVAVAADLLALTVLTPPGEFGADVAIGSAQRFGVP 274
                                                   ***************************************************************** PP

                                     TIGR00461 260 lGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvll 324
                                                   lG+GGphaa+f++kd +kr +pGr+vGvs d+ G++alrla+qtreqhirr+katsnictaqvll
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 275 LGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLL 339
                                                   ***************************************************************** PP

                                     TIGR00461 325 anvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlka 389
                                                   an+as+yavyhGpkGlk+ia+ri++lt+ila+gl   +++++++++fdtlt+  g ++a ++  +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 340 ANIASMYAVYHGPKGLKQIANRIHHLTAILAKGLSALGLNVEQANFFDTLTLATGANTA-ALHDK 403
                                                   ******************************************************99988.89999 PP

                                     TIGR00461 390 aeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpaellrdd 454
                                                   a+++ inlr ++ + +g++ldettt++d++ l+ vla  + l+ +   l   v++ +pael r++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 404 ARAQRINLRVIDGERLGLSLDETTTQADIETLWSVLADGKALP-DFAALAASVQSRIPAELVRQS 467
                                                   9***********************************9866554.8899***************** PP

                                     TIGR00461 455 eilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpf 519
                                                    il ++vfnryhsetel+ryl +l  kdlal+++miplGsctmklna+ em+p+tw ef+ +hpf
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 468 PILSHPVFNRYHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPF 532
                                                   ***************************************************************** PP

                                     TIGR00461 520 apaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclip 584
                                                   ap+ q+ Gy++l  +le+ l+  tG+daislqpn+G+qGeyaGl +ir yh+srgee+r+iclip
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 533 APPAQSAGYQQLTDELEAMLCAATGYDAISLQPNAGSQGEYAGLLAIRAYHQSRGEERRDICLIP 597
                                                   ***************************************************************** PP

                                     TIGR00461 585 asahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetire 649
                                                    sahGtnpa+a+maG++vv+ +cd  Gn+d++dl+aka ++ ++laa+m+typst+Gvfee+ire
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 598 SSAHGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIRE 662
                                                   ***************************************************************** PP

                                     TIGR00461 650 vidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshla 714
                                                   ++ i+h  GGqvy+dGanmna vGl++pg++G dv+hlnlhktf+iphGGGGpg+gpigvkshl+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 663 ICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLT 727
                                                   ***************************************************************** PP

                                     TIGR00461 715 pflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanyla 779
                                                   pflp+          +++++ gav aap+Gsasilpi++myi+mmG  Glk+as++ailnany+ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 728 PFLPG--------HAAMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNANYIS 784
                                                   *****........4688999********************************************* PP

                                     TIGR00461 780 krlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmve 844
                                                   +rl+++y++l++g+++ vahecildlr+lk+ +gi++ dvakrl+d+Gfhapt+sfpvaGtlm+e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 785 RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGTLMIE 849
                                                   ***************************************************************** PP

                                     TIGR00461 845 ptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaay 909
                                                   pteses+eeldrf+dami+i+eei av +G+++++dn+lknaph+   +iv+ew++pysre+a+y
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 850 PTESESKEELDRFCDAMICIREEIRAVENGTLDKDDNPLKNAPHT-AAEIVGEWTHPYSREQAVY 913
                                                   ********************************************5.6789*************** PP

                                     TIGR00461 910 papvlkyfkfwptvarlddtyGdrnlvcsc 939
                                                   p++ l + k+wp v+r+d+++Gdrnl+c+c
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03500 914 PVASLIEGKYWPPVGRVDNVFGDRNLICAC 943
                                                   *****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (950 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 10.92
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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