Alignments for a candidate for astA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Pseudomonas simiae WCS417

Align Arginine N-succinyltransferase subunit alpha; ARUAI; EC 2.3.1.109; AOST; AST (uncharacterized)
to candidate GFF4237 PS417_21705 arginine N-succinyltransferase

Query= curated2:P80357
         (338 letters)



>FitnessBrowser__WCS417:GFF4237
          Length = 339

 Score =  565 bits (1456), Expect = e-166
 Identities = 285/339 (84%), Positives = 309/339 (91%), Gaps = 1/339 (0%)

Query: 1   MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60
           MLVMRPAQ ADL +VQRLAADSP+GVTSLPDD ERL DKI ASEASFAAEVS+NGEESYF
Sbjct: 1   MLVMRPAQMADLGEVQRLAADSPIGVTSLPDDVERLSDKIAASEASFAAEVSFNGEESYF 60

Query: 61  FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120
           FVLED+ +G+L GCSAIVASAG+SEPFYSFRNETFVHASR L IHNKIHVLS CHDLTGN
Sbjct: 61  FVLEDTETGKLAGCSAIVASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSQCHDLTGN 120

Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180
           SLLTSFYV  +LV S ++ELNSRGRLLF+ASHPERFAD+VV EIVGYSDE G+SPFW+A+
Sbjct: 121 SLLTSFYVVPELVGSPWSELNSRGRLLFVASHPERFADSVVTEIVGYSDENGDSPFWDAI 180

Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240
           GRNFFDLNY  AE+L GLKSRTFLAELMPHYPIYVPLLPD AQE+MGQVHPRAQITFDIL
Sbjct: 181 GRNFFDLNYAAAERLCGLKSRTFLAELMPHYPIYVPLLPDEAQEAMGQVHPRAQITFDIL 240

Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPKS-GRPYLVTNGQLQD 299
           MREGFETD+YIDIFDGGPTLHAR SGIRSIAQSRVVPVKIGE  K  GR YLV+N QLQD
Sbjct: 241 MREGFETDHYIDIFDGGPTLHARVSGIRSIAQSRVVPVKIGEMVKGVGRQYLVSNAQLQD 300

Query: 300 FRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338
           +RAV+L+LD+APGKPV L + AAEALGVGEGASVRLVAV
Sbjct: 301 YRAVMLELDYAPGKPVTLDLAAAEALGVGEGASVRLVAV 339


Lambda     K      H
   0.319    0.135    0.387 

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: 437
Number of extensions: 9
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: 338
Length of database: 339
Length adjustment: 28
Effective length of query: 310
Effective length of database: 311
Effective search space:    96410
Effective search space used:    96410
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: 49 (23.5 bits)

Align candidate GFF4237 PS417_21705 (arginine N-succinyltransferase)
to HMM TIGR03245 (aruF: arginine/ornithine succinyltransferase, alpha subunit (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/TIGR03245.hmm
# target sequence database:        /tmp/gapView.13497.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03245  [M=336]
Accession:   TIGR03245
Description: arg_AOST_alph: arginine/ornithine succinyltransferase, alpha subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   8.7e-171  553.9   0.0   9.8e-171  553.8   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4237  PS417_21705 arginine N-succinylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4237  PS417_21705 arginine N-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.8   0.0  9.8e-171  9.8e-171       1     336 []       3     339 .]       3     339 .] 0.99

  Alignments for each domain:
  == domain 1  score: 553.8 bits;  conditional E-value: 9.8e-171
                           TIGR03245   1 vvrParladldaierlaresaigvtslPadrekleekiaqsessfaaevsfsgeesylfvledsetgkllGtasi 75 
                                         v+rPa++adl +++rla++s+igvtslP+d e+l +kia+se sfaaevsf+geesy+fvled+etgkl+G+++i
  lcl|FitnessBrowser__WCS417:GFF4237   3 VMRPAQMADLGEVQRLAADSPIGVTSLPDDVERLSDKIAASEASFAAEVSFNGEESYFFVLEDTETGKLAGCSAI 77 
                                         79************************************************************************* PP

                           TIGR03245  76 vasaGyaePfysyrndtlvhasrelkvnnkihvlslsheltGksllasfyvdpelreaeaaellsrarllfiaae 150
                                         vasaGy+ePfys+rn+t+vhasrelk++nkihvls +h+ltG+sll+sfyv pel+++ + el+sr+rllf+a++
  lcl|FitnessBrowser__WCS417:GFF4237  78 VASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSQCHDLTGNSLLTSFYVVPELVGSPWSELNSRGRLLFVASH 152
                                         *************************************************************************** PP

                           TIGR03245 151 rerfasrviaellGvsdeaGesPfWdaiGrkffdldfaaverasglksktfiaelmPsyPiyvpllpdeaqealg 225
                                         +erfa++v++e++G sde+G+sPfWdaiGr+ffdl++aa+er++glks+tf+aelmP+yPiyvpllpdeaqea+g
  lcl|FitnessBrowser__WCS417:GFF4237 153 PERFADSVVTEIVGYSDENGDSPFWDAIGRNFFDLNYAAAERLCGLKSRTFLAELMPHYPIYVPLLPDEAQEAMG 227
                                         *************************************************************************** PP

                           TIGR03245 226 qvheraelafdlllreGfeadryidifdgGpvleaeldrlktvkksrekpvkieeaatgg.stylvsnglledfr 299
                                         qvh+ra+++fd+l+reGfe+d+yidifdgGp+l+a++++++++++sr++pvki e  +g  ++ylvsn +l+d+r
  lcl|FitnessBrowser__WCS417:GFF4237 228 QVHPRAQITFDILMREGFETDHYIDIFDGGPTLHARVSGIRSIAQSRVVPVKIGEMVKGVgRQYLVSNAQLQDYR 302
                                         ********************************************************99999************** PP

                           TIGR03245 300 avladlavvdGkalrlkadaaealgvseGdavrlval 336
                                         av+++l+ ++Gk+++l+ +aaealgv+eG++vrlva+
  lcl|FitnessBrowser__WCS417:GFF4237 303 AVMLELDYAPGKPVTLDLAAAEALGVGEGASVRLVAV 339
                                         **********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (336 nodes)
Target sequences:                          1  (339 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.58
//
[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