Alignments for a candidate for astA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Pseudomonas putida KT2440

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate PP_4480 PP_4480 arginine N-succinyltransferase, subunit alpha

Query= SwissProt::Q8ZPV1
         (344 letters)



>FitnessBrowser__Putida:PP_4480
          Length = 339

 Score =  243 bits (621), Expect = 4e-69
 Identities = 139/338 (41%), Positives = 203/338 (60%), Gaps = 4/338 (1%)

Query: 1   MRVIRPVEHADIAALMQLAGKTGGGLTSLPANEATLAARIERALKTWSGELP-KGEQGYV 59
           M V+RP + AD+  + ++A  +  G+TSLP + A L  +I  +  +++ E+   GE+ Y 
Sbjct: 1   MLVMRPAQMADLNDVQRMAADSPIGVTSLPDDTARLGDKIAASETSFAAEVSFNGEESYF 60

Query: 60  FVLEDSETGEVGGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGS 119
           FVLEDSETG++ G  AI  + G ++P+Y++R  T VHAS+EL ++N +  L L +D TG+
Sbjct: 61  FVLEDSETGKLAGCSAIVASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSLCHDLTGN 120

Query: 120 SELCTLFLDPEWRKEGNGYLLSKSRFMFMAAFRDKFNEKVVAEMRGVIDEHGYSPFWQSL 179
           S L + ++ PE    G   L S+ R +FMAA  ++F + VV E+ G  DE G SPFW ++
Sbjct: 121 SLLTSFYVAPELVNSGWAELNSRGRLLFMAAHPERFADSVVTEIVGFSDEQGESPFWDAI 180

Query: 180 GKRFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSEEAQAVIGEVHPQTAPARAVL 239
           G+ FF ++++ A+ LCG   + F+AELMP +PIY   L + AQ  +G+VHP+      +L
Sbjct: 181 GRNFFDLNYADAERLCGLKSRTFLAELMPHYPIYVPLLPDLAQEAMGQVHPRAQITFDIL 240

Query: 240 EKEGFRYRHYIDIFDGGPTLECDIDRVRAIRKSRLVEV-AEGQPAPGDYPACLVANENYH 298
            +EGF   HYIDIFDGGPTL      +R+I +SR+V V  E  P  G  P  LV N    
Sbjct: 241 MREGFETEHYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIEEAPVKGGRP-YLVCNGLLQ 299

Query: 299 HFRAALVRADPQTSRLV-LTAAQLDALKCRAGDHVRLV 335
            +RA L+  D    + V L+ A  DAL    G  VRLV
Sbjct: 300 DYRAVLLDLDWVPGKPVSLSVAAADALGVGEGASVRLV 337


Lambda     K      H
   0.321    0.137    0.416 

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: 295
Number of extensions: 12
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: 344
Length of database: 339
Length adjustment: 29
Effective length of query: 315
Effective length of database: 310
Effective search space:    97650
Effective search space used:    97650
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate PP_4480 PP_4480 (arginine N-succinyltransferase, subunit alpha)
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.20508.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.3e-180  584.2   0.0   5.9e-180  584.1   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4480  PP_4480 arginine N-succinyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4480  PP_4480 arginine N-succinyltransferase, subunit alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  584.1   0.0  5.9e-180  5.9e-180       1     336 []       3     339 .]       3     339 .] 1.00

  Alignments for each domain:
  == domain 1  score: 584.1 bits;  conditional E-value: 5.9e-180
                           TIGR03245   1 vvrParladldaierlaresaigvtslPadrekleekiaqsessfaaevsfsgeesylfvledsetgkllGtasi 75 
                                         v+rPa++adl++++r+a++s+igvtslP+d+++l++kia+se+sfaaevsf+geesy+fvledsetgkl+G+++i
  lcl|FitnessBrowser__Putida:PP_4480   3 VMRPAQMADLNDVQRMAADSPIGVTSLPDDTARLGDKIAASETSFAAEVSFNGEESYFFVLEDSETGKLAGCSAI 77 
                                         79************************************************************************* PP

                           TIGR03245  76 vasaGyaePfysyrndtlvhasrelkvnnkihvlslsheltGksllasfyvdpelreaeaaellsrarllfiaae 150
                                         vasaGy+ePfys+rn+t+vhasrelk++nkihvlsl+h+ltG+sll+sfyv+pel+++ +ael+sr+rllf+aa+
  lcl|FitnessBrowser__Putida:PP_4480  78 VASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSLCHDLTGNSLLTSFYVAPELVNSGWAELNSRGRLLFMAAH 152
                                         *************************************************************************** PP

                           TIGR03245 151 rerfasrviaellGvsdeaGesPfWdaiGrkffdldfaaverasglksktfiaelmPsyPiyvpllpdeaqealg 225
                                         +erfa++v++e++G+sde+GesPfWdaiGr+ffdl++a++er++glks+tf+aelmP+yPiyvpllpd aqea+g
  lcl|FitnessBrowser__Putida:PP_4480 153 PERFADSVVTEIVGFSDEQGESPFWDAIGRNFFDLNYADAERLCGLKSRTFLAELMPHYPIYVPLLPDLAQEAMG 227
                                         *************************************************************************** PP

                           TIGR03245 226 qvheraelafdlllreGfeadryidifdgGpvleaeldrlktvkksrekpvkieeaatgg.stylvsnglledfr 299
                                         qvh+ra+++fd+l+reGfe+++yidifdgGp+l+a++++++++++sr++pvkieea+++g ++ylv+ngll+d+r
  lcl|FitnessBrowser__Putida:PP_4480 228 QVHPRAQITFDILMREGFETEHYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIEEAPVKGgRPYLVCNGLLQDYR 302
                                         *********************************************************9999************** PP

                           TIGR03245 300 avladlavvdGkalrlkadaaealgvseGdavrlval 336
                                         avl+dl++v+Gk+++l+++aa+algv+eG++vrlva+
  lcl|FitnessBrowser__Putida:PP_4480 303 AVLLDLDWVPGKPVSLSVAAADALGVGEGASVRLVAV 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 10.38
//
[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