Alignments for a candidate for astC in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for astC in Escherichia coli BW25113

Align succinylornithine transaminase; EC 2.6.1.81 (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)

Query= CharProtDB::CH_002469
         (406 letters)



>FitnessBrowser__Keio:15866
          Length = 406

 Score =  820 bits (2119), Expect = 0.0
 Identities = 406/406 (100%), Positives = 406/406 (100%)

Query: 1   MSQPITRENFDEWMIPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPEL 60
           MSQPITRENFDEWMIPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPEL
Sbjct: 1   MSQPITRENFDEWMIPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPEL 60

Query: 61  REALNEQASKFWHTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFA 120
           REALNEQASKFWHTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFA
Sbjct: 61  REALNEQASKFWHTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFA 120

Query: 121 HDRYGSHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALI 180
           HDRYGSHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALI
Sbjct: 121 HDRYGSHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALI 180

Query: 181 DDSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMH 240
           DDSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMH
Sbjct: 181 DDSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMH 240

Query: 241 YGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELIN 300
           YGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELIN
Sbjct: 241 YGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELIN 300

Query: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAK 360
           TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAK
Sbjct: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAK 360

Query: 361 AGVMVLIAGGNVVRFAPALNVSEEEVTTGLDRFAAACEHFVSRGSS 406
           AGVMVLIAGGNVVRFAPALNVSEEEVTTGLDRFAAACEHFVSRGSS
Sbjct: 361 AGVMVLIAGGNVVRFAPALNVSEEEVTTGLDRFAAACEHFVSRGSS 406


Lambda     K      H
   0.319    0.136    0.407 

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: 724
Number of extensions: 13
Number of successful extensions: 1
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: 406
Length of database: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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: 50 (23.9 bits)

Align candidate 15866 b1748 (succinylornithine transaminase, PLP-dependent (NCBI))
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

# 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/TIGR03246.hmm
# target sequence database:        /tmp/gapView.28716.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03246  [M=397]
Accession:   TIGR03246
Description: arg_catab_astC: succinylornithine transaminase family
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   7.8e-233  758.5   0.4   8.8e-233  758.3   0.4    1.0  1  lcl|FitnessBrowser__Keio:15866  b1748 succinylornithine transami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15866  b1748 succinylornithine transaminase, PLP-dependent (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  758.3   0.4  8.8e-233  8.8e-233       1     397 []       5     401 ..       5     401 .. 1.00

  Alignments for each domain:
  == domain 1  score: 758.3 bits;  conditional E-value: 8.8e-233
                       TIGR03246   1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytnepv 79 
                                     ++re+fde+m+pvyapa+fipvrgeGsr+wdq+gkeyidfaGGiavnalGhahpel+eal+eqa+k+wh+gngytnepv
  lcl|FitnessBrowser__Keio:15866   5 ITRENFDEWMIPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEPV 83 
                                     79***************************************************************************** PP

                       TIGR03246  80 lrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfaplp 158
                                     lrlakkl+datfad+vffcnsGaeaneaalklark+a+d+yg++ks ivafkn+fhGrtlftvs+GGq++ys+dfaplp
  lcl|FitnessBrowser__Keio:15866  84 LRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLP 162
                                     ******************************************************************************* PP

                       TIGR03246 159 egikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGelyaymey 237
                                     ++i+haaynd+++++ali+d+tcavivepiqGegGvvpa++afl+glrelc+rhnallifdevqtGvGrtGelyaym+y
  lcl|FitnessBrowser__Keio:15866 163 ADIRHAAYNDINSASALIDDSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHY 241
                                     ******************************************************************************* PP

                       TIGR03246 238 GvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvdele 316
                                     Gvtpd+lt+akalGgGfp+Gall+tee+a+v++vGthGttyGGnpla+ava+kvl+l+nt+e+l+Gvkqrh++fv++l+
  lcl|FitnessBrowser__Keio:15866 242 GVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEMLNGVKQRHDWFVERLN 320
                                     ******************************************************************************* PP

                       TIGR03246 317 kinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarlekavek 395
                                     +in+ry +fse+rG GlliG+vl+++yaG+ak++ ++aa++Gv+vliaG++vvrfap+l+++eee+++Gl+r++ a+e+
  lcl|FitnessBrowser__Keio:15866 321 TINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVMVLIAGGNVVRFAPALNVSEEEVTTGLDRFAAACEH 399
                                     *****************************************************************************99 PP

                       TIGR03246 396 lv 397
                                     +v
  lcl|FitnessBrowser__Keio:15866 400 FV 401
                                     86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (406 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: 00:00:00.02
# Mc/sec: 6.59
//
[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