Alignments for a candidate for rocF in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocF in Azospirillum brasilense Sp245

Align arginase subunit (EC 3.5.3.1) (characterized)
to candidate AZOBR_RS19585 AZOBR_RS19585 arginase

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



>FitnessBrowser__azobra:AZOBR_RS19585
          Length = 315

 Score =  325 bits (833), Expect = 9e-94
 Identities = 168/308 (54%), Positives = 214/308 (69%), Gaps = 10/308 (3%)

Query: 22  QILGAPVQSGASQPGCLMGPDAFRTAGLTQVLTELGWAVTDLGDA-----TPTVEPELSH 76
           +I+G P+++GA  PG LMGP A RTAGL + L ELG  V DLGD      TP      S 
Sbjct: 2   EIIGVPIEAGAGHPGALMGPAALRTAGLVRALRELGHEVRDLGDLGRGDLTPA---PWSE 58

Query: 77  PNSAVKNLDALVGWTRSLSQKALEMARSCDLPVFLGGDHSMSAGTVSGVAQRTAELGKEQ 136
            ++A   L  +  W+R+L+ ++  M ++  +PVFLGGDHS+S G+V+GVA+   E GK  
Sbjct: 59  GDAATARLAEITAWSRALADRSYAMMQAGGVPVFLGGDHSLSMGSVTGVARHCRETGKPL 118

Query: 137 FVLWLDAHTDLHTLHTTASGNLHGTPVAYYTGQSGFEGL--PPLAAPVNPRNVSMMGIRS 194
           FVLWLDAH D +T HT+ SGN+HG PVA   G+ GF+ +  P   A VNP +V + GIRS
Sbjct: 119 FVLWLDAHGDFNTPHTSPSGNMHGMPVALLCGEDGFDNVFPPEQRATVNPAHVHLFGIRS 178

Query: 195 VDPEERRRVAEIGVQVADMRVLDEQGVVRPLEAFLDRVSKVSGRLHVSLDVDFLDPAIAP 254
           +DP ERR +   GV V DMR++DE GV   +   ++RV +  G LHVSLDVDFLDPAIAP
Sbjct: 179 LDPGERRLLRARGVDVVDMRLIDEHGVGVHMRRIIERVRQAGGHLHVSLDVDFLDPAIAP 238

Query: 255 AVGTTVPGGATFREAHLIMEMLHDSGLVTSLDLAELNPFLDERGRTARLITDLASSLFGR 314
           AVGT V GGAT+REAHLIMEMLHD+G+V SLD+ ELNPFLDERG++A L+ DL +SLFGR
Sbjct: 239 AVGTAVLGGATYREAHLIMEMLHDAGVVGSLDVVELNPFLDERGKSALLLVDLVASLFGR 298

Query: 315 RVFDRVTT 322
           R+ D   T
Sbjct: 299 RIIDPAVT 306


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: 341
Number of extensions: 17
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: 324
Length of database: 315
Length adjustment: 28
Effective length of query: 296
Effective length of database: 287
Effective search space:    84952
Effective search space used:    84952
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 AZOBR_RS19585 AZOBR_RS19585 (arginase)
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.2763.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.1e-89  286.8   0.0    1.2e-89  286.6   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS19585  AZOBR_RS19585 arginase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS19585  AZOBR_RS19585 arginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.6   0.0   1.2e-89   1.2e-89       2     298 ..       3     299 ..       2     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: 286.6 bits;  conditional E-value: 1.2e-89
                                 TIGR01229   2 ivglpfseGqgkrGvdkGpkalreaglleklkdlekevedlgqvaaaklekesd...reavkaersvla 67 
                                               i+g+p++ G+g+ G  +Gp alr agl+ +l++l++ev+dlg++   +l+       + a   +  ++a
  lcl|FitnessBrowser__azobra:AZOBR_RS19585   3 IIGVPIEAGAGHPGALMGPAALRTAGLVRALRELGHEVRDLGDLGRGDLTPAPWsegDAATARLAEITA 71 
                                               9*******************************************9777766543334666677777*** PP

                                 TIGR01229  68 akeklaekvkkvveekrfplvLggdHsiaiGtvsgvakkakdk..klgvlwlDAHaDintletstSgnl 134
                                               ++++la+  + +++++ +p++LggdHs+ +G+v+gva++ ++    l+vlwlDAH+D+nt++ts+Sgn+
  lcl|FitnessBrowser__azobra:AZOBR_RS19585  72 WSRALADRSYAMMQAGGVPVFLGGDHSLSMGSVTGVARHCRETgkPLFVLWLDAHGDFNTPHTSPSGNM 140
                                               ****************************************997768*********************** PP

                                 TIGR01229 135 HGmPlafllgrlkkevedleelkllkgkeispkklvyiGlRdvdegErkilkelgikvfsmkeidklGi 203
                                               HGmP+a+l g+ ++++   +e    ++ +++p ++ ++G+R++d+gEr++l+  g+ v +m+ id++G+
  lcl|FitnessBrowser__azobra:AZOBR_RS19585 141 HGMPVALLCGEDGFDNVFPPE---QRA-TVNPAHVHLFGIRSLDPGERRLLRARGVDVVDMRLIDEHGV 205
                                               **********99999866666...556.6**************************************** PP

                                 TIGR01229 204 akvvektleslkaed.pihlSlDvDglDpklapatGtpvrgGltfrEgklilelllesglltaldlvEv 271
                                               +  +++ +e++++    +h+SlDvD+lDp +apa+Gt v gG+t+rE++li+e+l+++g + +ld+vE+
  lcl|FitnessBrowser__azobra:AZOBR_RS19585 206 GVHMRRIIERVRQAGgHLHVSLDVDFLDPAIAPAVGTAVLGGATYREAHLIMEMLHDAGVVGSLDVVEL 274
                                               ************9999***************************************************** PP

                                 TIGR01229 272 NPtldikeksetikaavelvesllget 298
                                               NP+ld  e+++ +   v+lv+sl+g+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS19585 275 NPFLD--ERGKSALLLVDLVASLFGRR 299
                                               *****..9****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (315 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.97
//
[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