Alignments for a candidate for rocF in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocF in Sinorhizobium meliloti 1021

Align arginase subunit (EC 3.5.3.1) (characterized)
to candidate SMc03091 SMc03091 arginase

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



>FitnessBrowser__Smeli:SMc03091
          Length = 307

 Score =  312 bits (799), Expect = 8e-90
 Identities = 156/308 (50%), Positives = 213/308 (69%), Gaps = 4/308 (1%)

Query: 18  LKTCQILGAPVQSGASQPGCLMGPDAFRTAGLTQVLTELGWAVTDLGDATPTVEPELS-H 76
           +KT  ++GAP++ G+ + G  MGP A R AG+  VL ELG  V D GD  P    +L+ H
Sbjct: 1   MKTITLIGAPIEEGSGRRGAAMGPTALRIAGIDTVLAELGHTVNDEGDLRPLPARDLANH 60

Query: 77  PNSAVKNLDALVGWTRSLSQKALEMARSCDLPVFLGGDHSMSAGTVSGVAQRTAELGKEQ 136
           P +   NL ++  + R+L +   + AR    P+ LGGDH++S G+VSG+A+   ++G+  
Sbjct: 61  PGA--NNLQSVAAFARALDEAVHDTARKGHFPIILGGDHALSMGSVSGMARHAQDVGRPL 118

Query: 137 FVLWLDAHTDLHTLHTTASGNLHGTPVAYYTGQSGFEGLPPLAAP-VNPRNVSMMGIRSV 195
           FVLWLDAH D ++  T+ SGN+HG PVA++ G++ F  + P   P V+P+ V  +GIRSV
Sbjct: 119 FVLWLDAHADFNSPATSPSGNMHGMPVAFFCGEAEFAPILPKDRPLVDPKKVYQVGIRSV 178

Query: 196 DPEERRRVAEIGVQVADMRVLDEQGVVRPLEAFLDRVSKVSGRLHVSLDVDFLDPAIAPA 255
           D  ER  +AE GV V DMR +DE G+   +   +D V   +G LHVSLDVDF+DP +AP 
Sbjct: 179 DAREREEIAEHGVNVFDMRAIDEMGMAHIIRQIVDEVRAANGLLHVSLDVDFMDPELAPG 238

Query: 256 VGTTVPGGATFREAHLIMEMLHDSGLVTSLDLAELNPFLDERGRTARLITDLASSLFGRR 315
           VGTTVPGGATFREAHLIME+L DSGLV+SLD+ ELNPFLD+RG++AR++ +L +SLFGRR
Sbjct: 239 VGTTVPGGATFREAHLIMEVLCDSGLVSSLDVVELNPFLDDRGKSARILVELTASLFGRR 298

Query: 316 VFDRVTTA 323
           + DR T A
Sbjct: 299 ILDRPTRA 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: 272
Number of extensions: 12
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: 307
Length adjustment: 27
Effective length of query: 297
Effective length of database: 280
Effective search space:    83160
Effective search space used:    83160
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 SMc03091 SMc03091 (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.29639.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    6.1e-97  310.5   0.0      7e-97  310.3   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc03091  SMc03091 arginase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03091  SMc03091 arginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.3   0.0     7e-97     7e-97       2     298 ..       6     298 ..       5     300 .. 0.96

  Alignments for each domain:
  == domain 1  score: 310.3 bits;  conditional E-value: 7e-97
                           TIGR01229   2 ivglpfseGqgkrGvdkGpkalreaglleklkdlekevedlgqvaaaklekesdreavkaersvlaakeklaekv 76 
                                         ++g+p++eG g+rG  +Gp+alr ag+ + l +l+++v+d g+++ +      ++ + ++++sv a  ++l e+v
  lcl|FitnessBrowser__Smeli:SMc03091   6 LIGAPIEEGSGRRGAAMGPTALRIAGIDTVLAELGHTVNDEGDLRPLPARDLANHPGANNLQSVAAFARALDEAV 80 
                                         79*******************************************888888889********************* PP

                           TIGR01229  77 kkvveekrfplvLggdHsiaiGtvsgvakkakdk..klgvlwlDAHaDintletstSgnlHGmPlafllgrlkke 149
                                         +  +++++fp++LggdH++ +G+vsg+a++a+d    l+vlwlDAHaD+n + ts+Sgn+HGmP+af+ g+   e
  lcl|FitnessBrowser__Smeli:SMc03091  81 HDTARKGHFPIILGGDHALSMGSVSGMARHAQDVgrPLFVLWLDAHADFNSPATSPSGNMHGMPVAFFCGE--AE 153
                                         *********************************7669*********************************4..44 PP

                           TIGR01229 150 v.edleelkllkgkeispkklvyiGlRdvdegErkilkelgikvfsmkeidklGiakvvektleslkaed.pihl 222
                                         + + l++    ++  ++pkk+  +G+R+vd+ Er+ + e+g++vf+m++id++G+a+++++ +++++a + ++h+
  lcl|FitnessBrowser__Smeli:SMc03091 154 FaPILPK---DRP-LVDPKKVYQVGIRSVDAREREEIAEHGVNVFDMRAIDEMGMAHIIRQIVDEVRAANgLLHV 224
                                         5357777...788.8*****************************************************9999*** PP

                           TIGR01229 223 SlDvDglDpklapatGtpvrgGltfrEgklilelllesglltaldlvEvNPtldikeksetikaavelvesllge 297
                                         SlDvD++Dp+lap++Gt+v+gG+tfrE++li+e l +sgl+++ld+vE+NP+ld  ++++ ++  vel++sl+g+
  lcl|FitnessBrowser__Smeli:SMc03091 225 SLDVDFMDPELAPGVGTTVPGGATFREAHLIMEVLCDSGLVSSLDVVELNPFLD--DRGKSARILVELTASLFGR 297
                                         ******************************************************..99***************98 PP

                           TIGR01229 298 t 298
                                          
  lcl|FitnessBrowser__Smeli:SMc03091 298 R 298
                                         6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (300 nodes)
Target sequences:                          1  (307 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: 7.29
//
[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