GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcvP in Pseudomonas fluorescens FW300-N1B4

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate Pf1N1B4_621 Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
         (950 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 Glycine dehydrogenase
           [decarboxylating] (glycine cleavage system P protein)
           (EC 1.4.4.2)
          Length = 950

 Score = 1838 bits (4760), Expect = 0.0
 Identities = 915/950 (96%), Positives = 932/950 (98%)

Query: 1   MTQINLTTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL 60
           MTQINL TANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL
Sbjct: 1   MTQINLGTANEFIARHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGL 60

Query: 61  SEADALALIKSIATKNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQG 120
           SEADALALIKSIA KNQLFKT+IGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQG
Sbjct: 61  SEADALALIKSIAGKNQLFKTYIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQG 120

Query: 121 RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQ 180
           RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQ
Sbjct: 121 RLEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQ 180

Query: 181 TLDVLRTRAEPLGIDVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANAL 240
           TLDVLRTRAEPLGIDVVVGDEREL DVTPFFGALLQYPASNGDVFDYRELTERFHAANAL
Sbjct: 181 TLDVLRTRAEPLGIDVVVGDERELADVTPFFGALLQYPASNGDVFDYRELTERFHAANAL 240

Query: 241 VAVAADLLALTVLTAPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLV 300
           VAVAADLLALTVLT PGEFGADVAIGSAQRFGVPLGFGGPHAAYFST+DAFKRDMPGRLV
Sbjct: 241 VAVAADLLALTVLTPPGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTRDAFKRDMPGRLV 300

Query: 301 GVSVDRFGNPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIAN 360
           GVSVDRFG PALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIA 
Sbjct: 301 GVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIAQ 360

Query: 361 RVHHLTAILAKGLSALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLG 420
           R+HHLTAILAKGLS+LGL+VEQA+FFDTLT+K G  TA LHD+A AQ+INLRVVD ERLG
Sbjct: 361 RIHHLTAILAKGLSSLGLTVEQANFFDTLTIKTGVNTAKLHDQARAQQINLRVVDAERLG 420

Query: 421 LSLDETTTQADVETLWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHS 480
           LSLDETT+QADVETLWS+LS+GKALPDFAALAASV+S +PA LVRQSPILSHPVFNRYHS
Sbjct: 421 LSLDETTSQADVETLWSVLSEGKALPDFAALAASVESTLPAALVRQSPILSHPVFNRYHS 480

Query: 481 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG 540
           ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG
Sbjct: 481 ETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAG 540

Query: 541 YQQLTDELEAMLCAATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA 600
           YQQLTDELEAMLCAATGYDS+SLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA
Sbjct: 541 YQQLTDELEAMLCAATGYDSISLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSA 600

Query: 601 HGTNPATAQMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 660
           HGTNPATA MAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI
Sbjct: 601 HGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGI 660

Query: 661 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 720
           REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI
Sbjct: 661 REICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPI 720

Query: 721 GVKSHLAPFLPGHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNA 780
           GVKSHL PFLPGHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLK ASQLAILNA
Sbjct: 721 GVKSHLTPFLPGHAQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKCASQLAILNA 780

Query: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840
           NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF
Sbjct: 781 NYISRRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSF 840

Query: 841 PVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVG 900
           PVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTA E+VG
Sbjct: 841 PVAGTLMIEPTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAAEIVG 900

Query: 901 EWSHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 950
           EW+HPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA
Sbjct: 901 EWTHPYSREQAVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 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: 2638
Number of extensions: 97
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 Pf1N1B4_621 (Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2))
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.18040.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 1497.2   0.0          0 1497.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621  Glycine dehydrogenase [decarboxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621  Glycine dehydrogenase [decarboxylating] (glycine cleavage system P prot
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1497.0   0.0         0         0       1     939 []      15     943 ..      15     943 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1497.0 bits;  conditional E-value: 0
                                     TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkv 65 
                                                   rh+Gp + + + ml++lGfd+l+al   ++p++i+ +  l le   +e +ala +k+ia kn+ +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621  15 RHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEADALALIKSIAGKNQLF 79 
                                                   9**************************************************************** PP

                                     TIGR00461  66 ksyiGkGyyatilppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanas 130
                                                   k+yiG+Gyy+t +p  i+rnllenp wytaytpyqpeisqGrleallnfqt+++dltGl++anas
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621  80 KTYIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISDLTGLPIANAS 144
                                                   ***************************************************************** PP

                                     TIGR00461 131 lldegtaaaeamalsfrvskkk.ankfvvakdvhpqtlevvktraeplgievivddaskvkkavd 194
                                                   llde+taaaeam +++r+sk+k + +f+ + ++hpqtl+v++traeplgi+v+v+d +++ + + 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 145 LLDEATAAAEAMTFCKRLSKNKgSHAFFASVHCHPQTLDVLRTRAEPLGIDVVVGDERELADVTP 209
                                                   **********************8999*************************************** PP

                                     TIGR00461 195 vlGvllqypatdGeildykalidelksrkalvsvaadllaltlltppgklGadivlGsaqrfGvp 259
                                                    +G+llqypa++G+++dy++l+++ +  +alv+vaadllalt+ltppg++Gad+++GsaqrfGvp
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 210 FFGALLQYPASNGDVFDYRELTERFHAANALVAVAADLLALTVLTPPGEFGADVAIGSAQRFGVP 274
                                                   ***************************************************************** PP

                                     TIGR00461 260 lGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhirrdkatsnictaqvll 324
                                                   lG+GGphaa+f+++d +kr +pGr+vGvs d+ G++alrla+qtreqhirr+katsnictaqvll
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 275 LGFGGPHAAYFSTRDAFKRDMPGRLVGVSVDRFGKPALRLAMQTREQHIRREKATSNICTAQVLL 339
                                                   ***************************************************************** PP

                                     TIGR00461 325 anvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaasevlka 389
                                                   an+as+yavyhGpkGl +ia+ri++lt+ila+gl   ++ ++++++fdtlt++ g ++a ++  +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 340 ANIASMYAVYHGPKGLTQIAQRIHHLTAILAKGLSSLGLTVEQANFFDTLTIKTGVNTA-KLHDQ 403
                                                   *******************************************************9998.99*** PP

                                     TIGR00461 390 aeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpaellrdd 454
                                                   a++++inlr v+++ +g++ldett+++dv+ l+ vl+  + l+ +   l   v++++pa+l r++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 404 ARAQQINLRVVDAERLGLSLDETTSQADVETLWSVLSEGKALP-DFAALAASVESTLPAALVRQS 467
                                                   ************************************9866554.8899***************** PP

                                     TIGR00461 455 eilrdevfnryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpf 519
                                                    il ++vfnryhsetel+ryl +l  kdlal+++miplGsctmklna+ em+p+tw ef+ +hpf
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 468 PILSHPVFNRYHSETELMRYLRKLADKDLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPF 532
                                                   ***************************************************************** PP

                                     TIGR00461 520 apaeqveGykeliaqlekwlveitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclip 584
                                                   apaeq+ Gy++l  +le+ l+  tG+d+islqpn+G+qGeyaGl +ir yh+srge++r+iclip
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 533 APAEQSAGYQQLTDELEAMLCAATGYDSISLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIP 597
                                                   ***************************************************************** PP

                                     TIGR00461 585 asahGtnpasaamaGlkvvpvkcdkeGnidlvdlkakaekagdelaavmvtypstyGvfeetire 649
                                                    sahGtnpa+a+maG++vv+ +cd  Gn+d++dl+aka ++ ++laa+m+typst+Gvfee+ire
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 598 SSAHGTNPATANMAGMRVVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIRE 662
                                                   ***************************************************************** PP

                                     TIGR00461 650 vidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktfsiphGGGGpgmgpigvkshla 714
                                                   ++ i+h  GGqvy+dGanmna vGl++pg++G dv+hlnlhktf+iphGGGGpg+gpigvkshl+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 663 ICGIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLT 727
                                                   ***************************************************************** PP

                                     TIGR00461 715 pflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasevailnanyla 779
                                                   pflp++          ++++ gav aap+Gsasilpi++myi+mmG  Glk as++ailnany+ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 728 PFLPGH--------AQMERKEGAVCAAPFGSASILPITWMYIRMMGGAGLKCASQLAILNANYIS 784
                                                   *****4........4567889******************************************** PP

                                     TIGR00461 780 krlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmve 844
                                                   +rl+++y++l++g+++ vahecildlr+lk+ +gi++ dvakrl+d+Gfhapt+sfpvaGtlm+e
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 785 RRLEEHYPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGTLMIE 849
                                                   ***************************************************************** PP

                                     TIGR00461 845 ptesesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaay 909
                                                   pteses+eeldrf+dami i+eei av +G+++++dn+lknaph+   +iv+ew++pysre+a+y
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 850 PTESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHT-AAEIVGEWTHPYSREQAVY 913
                                                   ********************************************5.6789*************** PP

                                     TIGR00461 910 papvlkyfkfwptvarlddtyGdrnlvcsc 939
                                                   p++ l + k+wp v+r+d+++Gdrnlvc+c
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_621 914 PVASLIEGKYWPPVGRVDNVFGDRNLVCAC 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 11.90
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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