Alignments for a candidate for rocF in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocF in Phaeobacter inhibens BS107

Align arginase subunit (EC 3.5.3.1) (characterized)
to candidate GFF1615 PGA1_c16370 arginase ArcA

Query= metacyc::MONOMER-11552
         (324 letters)



>FitnessBrowser__Phaeo:GFF1615
          Length = 310

 Score =  346 bits (887), Expect = e-100
 Identities = 179/307 (58%), Positives = 215/307 (70%), Gaps = 4/307 (1%)

Query: 19  KTCQILGAPVQSGASQPGCLMGPDAFRTAGLTQVLTELGWAVTDLGDATP-TVEPELSHP 77
           KTC ++GAPV SG  + GCLMGPDA+RTAGL + +  LG  V D G+  P T EP+ +  
Sbjct: 6   KTCILIGAPVDSGKRRAGCLMGPDAYRTAGLGRAIESLGHKVIDQGNLRPATHEPDTNDG 65

Query: 78  NSAVKNLDALVGWTRSLSQKALEMARSCDLPVFLGGDHSMSAGTVSGVAQRTAELGKEQF 137
               +N    +GWT  L  +A E A    LP+FLGGDHS+S G+V GVA   A+ G+ QF
Sbjct: 66  LVFARN--ETIGWTNRLI-RAAEEAMKDGLPIFLGGDHSLSLGSVVGVANHAAKEGRPQF 122

Query: 138 VLWLDAHTDLHTLHTTASGNLHGTPVAYYTGQSGFEGLPPLAAPVNPRNVSMMGIRSVDP 197
           VLWLDAHTD HT  T+ SGNLHGTPV Y+TG+  F G P +A PV   NV M+G+RSVD 
Sbjct: 123 VLWLDAHTDFHTPATSDSGNLHGTPVGYFTGRPDFAGFPEVANPVPQENVCMIGLRSVDT 182

Query: 198 EERRRVAEIGVQVADMRVLDEQGVVRPLEAFLDRVSKVSGRLHVSLDVDFLDPAIAPAVG 257
            ER  +    +   DMR +DE G+  PL AFL RV   +G LHVSLDVDFLDP++APAVG
Sbjct: 183 PERLALEASDIHRHDMRDIDENGIAGPLSAFLQRVKDANGMLHVSLDVDFLDPSVAPAVG 242

Query: 258 TTVPGGATFREAHLIMEMLHDSGLVTSLDLAELNPFLDERGRTARLITDLASSLFGRRVF 317
           TTVPGGAT RE HL+ EMLHDSGL+TSLDL ELNPFLDERGRTA L+ DL +S  GRRVF
Sbjct: 243 TTVPGGATVREGHLVCEMLHDSGLMTSLDLVELNPFLDERGRTAHLMVDLCASALGRRVF 302

Query: 318 DRVTTAF 324
           DR T ++
Sbjct: 303 DRPTRSY 309


Lambda     K      H
   0.318    0.134    0.393 

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: 324
Number of extensions: 11
Number of successful extensions: 2
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: 324
Length of database: 310
Length adjustment: 27
Effective length of query: 297
Effective length of database: 283
Effective search space:    84051
Effective search space used:    84051
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate GFF1615 PGA1_c16370 (arginase ArcA)
to HMM TIGR01229 (rocF: arginase (EC 3.5.3.1))

# 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/TIGR01229.hmm
# target sequence database:        /tmp/gapView.11433.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01229  [M=300]
Accession:   TIGR01229
Description: rocF_arginase: arginase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    2.7e-90  288.7   0.0      3e-90  288.5   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1615  PGA1_c16370 arginase ArcA


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1615  PGA1_c16370 arginase ArcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.5   0.0     3e-90     3e-90       2     298 ..      10     300 ..       9     302 .. 0.96

  Alignments for each domain:
  == domain 1  score: 288.5 bits;  conditional E-value: 3e-90
                          TIGR01229   2 ivglpfseGqgkrGvdkGpkalreaglleklkdlekevedlgqvaaaklekesdreavkaersvlaakeklaekvk 77 
                                        ++g+p++ G+ + G+ +Gp+a+r agl  +++ l+++v d g+++ a+ e ++++  v a++    ++++l+++++
  lcl|FitnessBrowser__Phaeo:GFF1615  10 LIGAPVDSGKRRAGCLMGPDAYRTAGLGRAIESLGHKVIDQGNLRPATHEPDTNDGLVFARNETIGWTNRLIRAAE 85 
                                        89***************************************************9999999999************* PP

                          TIGR01229  78 kvveekrfplvLggdHsiaiGtvsgvakkakdk..klgvlwlDAHaDintletstSgnlHGmPlafllgrlkkeve 151
                                        + ++++ +p++LggdHs+ +G+v gva++a+     ++vlwlDAH+D++t+ ts+SgnlHG+P+++++g  + ++ 
  lcl|FitnessBrowser__Phaeo:GFF1615  86 EAMKDG-LPIFLGGDHSLSLGSVVGVANHAAKEgrPQFVLWLDAHTDFHTPATSDSGNLHGTPVGYFTG--RPDFA 158
                                        ***999.********************998776669*********************************..78888 PP

                          TIGR01229 152 dleelkllkgkeispkklvyiGlRdvdegErkilkelgikvfsmkeidklGiakvvektleslkaed.pihlSlDv 226
                                         ++e   ++ + +  +++++iGlR+vd  Er +l  ++i+ ++m++id++Gia  +  +l+++k  + ++h+SlDv
  lcl|FitnessBrowser__Phaeo:GFF1615 159 GFPE---VANP-VPQENVCMIGLRSVDTPERLALEASDIHRHDMRDIDENGIAGPLSAFLQRVKDANgMLHVSLDV 230
                                        8999...5554.899*************************************************9999******** PP

                          TIGR01229 227 DglDpklapatGtpvrgGltfrEgklilelllesglltaldlvEvNPtldikeksetikaavelvesllget 298
                                        D+lDp++apa+Gt+v+gG+t rEg+l+ e+l++sgl+t+ldlvE+NP+ld  e+++t++ +v+l +s+lg+ 
  lcl|FitnessBrowser__Phaeo:GFF1615 231 DFLDPSVAPAVGTTVPGGATVREGHLVCEMLHDSGLMTSLDLVELNPFLD--ERGRTAHLMVDLCASALGRR 300
                                        **************************************************..******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (310 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.31
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources