Alignments for a candidate for astA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Marinobacter adhaerens HP15

Align Arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate GFF3097 HP15_3040 arginine N-succinyltransferase subunit beta

Query= reanno::Marino:GFF3097
         (366 letters)



>FitnessBrowser__Marino:GFF3097
          Length = 366

 Score =  728 bits (1880), Expect = 0.0
 Identities = 366/366 (100%), Positives = 366/366 (100%)

Query: 1   MLVIRPLQENDLDDLYAMAQSAGKGLTTLPADRELLQKKINHARETFNQRIAPEAGLYLF 60
           MLVIRPLQENDLDDLYAMAQSAGKGLTTLPADRELLQKKINHARETFNQRIAPEAGLYLF
Sbjct: 1   MLVIRPLQENDLDDLYAMAQSAGKGLTTLPADRELLQKKINHARETFNQRIAPEAGLYLF 60

Query: 61  ALEDTERKKTVGISGIQARVGLDEVFYNYRLSVTVNASKELGVHVRTPTLHLSNDMTDTS 120
           ALEDTERKKTVGISGIQARVGLDEVFYNYRLSVTVNASKELGVHVRTPTLHLSNDMTDTS
Sbjct: 61  ALEDTERKKTVGISGIQARVGLDEVFYNYRLSVTVNASKELGVHVRTPTLHLSNDMTDTS 120

Query: 121 EICSLLLSDEYKGGGSGLLLSRCRFMYLDEFRKHFSEKIFAEMRGVSDANGRSPLWDALG 180
           EICSLLLSDEYKGGGSGLLLSRCRFMYLDEFRKHFSEKIFAEMRGVSDANGRSPLWDALG
Sbjct: 121 EICSLLLSDEYKGGGSGLLLSRCRFMYLDEFRKHFSEKIFAEMRGVSDANGRSPLWDALG 180

Query: 181 TKFFDMEFSEADMLSGLGNKSFIAELMPKYPIYLSMLPDSARAVIGRVHDNTAPALRMLQ 240
           TKFFDMEFSEADMLSGLGNKSFIAELMPKYPIYLSMLPDSARAVIGRVHDNTAPALRMLQ
Sbjct: 181 TKFFDMEFSEADMLSGLGNKSFIAELMPKYPIYLSMLPDSARAVIGRVHDNTAPALRMLQ 240

Query: 241 SEGFNFNGLVDIFDGGPVVEAFVHNVRTVREGMNRHAMVTRKPVNLDVPSEERVMVSNRS 300
           SEGFNFNGLVDIFDGGPVVEAFVHNVRTVREGMNRHAMVTRKPVNLDVPSEERVMVSNRS
Sbjct: 241 SEGFNFNGLVDIFDGGPVVEAFVHNVRTVREGMNRHAMVTRKPVNLDVPSEERVMVSNRS 300

Query: 301 FRDFRVTTVPIDCIGPDTVSLPPEVAEALQIESGDPVRLAPLKDSGLLTKHSYRSSVPGG 360
           FRDFRVTTVPIDCIGPDTVSLPPEVAEALQIESGDPVRLAPLKDSGLLTKHSYRSSVPGG
Sbjct: 301 FRDFRVTTVPIDCIGPDTVSLPPEVAEALQIESGDPVRLAPLKDSGLLTKHSYRSSVPGG 360

Query: 361 ASKWQS 366
           ASKWQS
Sbjct: 361 ASKWQS 366


Lambda     K      H
   0.319    0.136    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: 597
Number of extensions: 10
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: 366
Length of database: 366
Length adjustment: 30
Effective length of query: 336
Effective length of database: 336
Effective search space:   112896
Effective search space used:   112896
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate GFF3097 HP15_3040 (arginine N-succinyltransferase subunit beta)
to HMM TIGR03244 (astA: arginine N-succinyltransferase (EC 2.3.1.109))

# 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/TIGR03244.hmm
# target sequence database:        /tmp/gapView.22119.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03244  [M=336]
Accession:   TIGR03244
Description: arg_catab_AstA: arginine N-succinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.2e-137  442.8   0.0   3.7e-137  442.6   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3097  HP15_3040 arginine N-succinyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3097  HP15_3040 arginine N-succinyltransferase subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.6   0.0  3.7e-137  3.7e-137       1     335 [.       3     341 ..       3     342 .. 0.96

  Alignments for each domain:
  == domain 1  score: 442.6 bits;  conditional E-value: 3.7e-137
                           TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledtetgkvvGvsaie 75 
                                         ++rp++++dld+l+++a++aG+Glt+lpa++ell+k+i++a+++f+++++++   ylf ledte +k vG+s+i+
  lcl|FitnessBrowser__Marino:GFF3097   3 VIRPLQENDLDDLYAMAQSAGKGLTTLPADRELLQKKINHARETFNQRIAPEAGLYLFALEDTERKKTVGISGIQ 77 
                                         79************************************************************************* PP

                           TIGR03244  76 aavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrkelnGkllskarflflaefk 150
                                         a+vGl+e+fynyr++ +v+askel+++ +++tl lsnd+t++se+C+l l++ey+ +  G lls++rf++l ef+
  lcl|FitnessBrowser__Marino:GFF3097  78 ARVGLDEVFYNYRLSVTVNASKELGVHVRTPTLHLSNDMTDTSEICSLLLSDEYKGGGSGLLLSRCRFMYLDEFR 152
                                         *************************************************************************** PP

                           TIGR03244 151 erfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPiyvdllskeaqdvigk 225
                                         ++fs+ki+aemrGvsd +GrsP+W+alg+kff+++fs+ad lsg+G+k+fiaelmPk+Piy+++l++ a++vig+
  lcl|FitnessBrowser__Marino:GFF3097 153 KHFSEKIFAEMRGVSDANGRSPLWDALGTKFFDMEFSEADMLSGLGNKSFIAELMPKYPIYLSMLPDSARAVIGR 227
                                         *************************************************************************** PP

                           TIGR03244 226 vhektkPalalleseGlryqgyvdifdaGptleaevakiravreskl.vevavaesaaed..eaepylvanekle 297
                                         vh++t+Pal++l+seG++++g vdifd+Gp++ea v+++r+vre      + + ++++ d  ++e+++v+n++++
  lcl|FitnessBrowser__Marino:GFF3097 228 VHDNTAPALRMLQSEGFNFNGLVDIFDGGPVVEAFVHNVRTVREGMNrHAMVTRKPVNLDvpSEERVMVSNRSFR 302
                                         ********************************************8763555556666665335789********* PP

                           TIGR03244 298 dfrvvlvess.ldaeelvlsaeeakalkveeGdkvrvva 335
                                         dfrv++v+ + +  ++++l +e a+al++e+Gd vr+ +
  lcl|FitnessBrowser__Marino:GFF3097 303 DFRVTTVPIDcIGPDTVSLPPEVAEALQIESGDPVRLAP 341
                                         *********97789**********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (336 nodes)
Target sequences:                          1  (366 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.52
//
[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