Alignments for a candidate for astA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Pseudomonas fluorescens FW300-N1B4

Align Arginine N-succinyltransferase subunit alpha; ARUAI; EC 2.3.1.109; AOST; AST (uncharacterized)
to candidate Pf1N1B4_3442 Arginine N-succinyltransferase, alpha subunit (EC 2.3.1.109)

Query= curated2:P80357
         (338 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3442
          Length = 339

 Score =  574 bits (1479), Expect = e-168
 Identities = 289/339 (85%), Positives = 314/339 (92%), 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+A+G+LVGCSAIVASAG+SEPFYSFRNETFVHASR L IHNKIHVLS CHDLTGN
Sbjct: 61  FVLEDTATGKLVGCSAIVASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSQCHDLTGN 120

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

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

Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPK-SGRPYLVTNGQLQD 299
           MREGFETD+YIDIFDGGPTLHAR SGIRSIAQSRVVPVKIGE  K +GR YLV N QLQD
Sbjct: 241 MREGFETDHYIDIFDGGPTLHARVSGIRSIAQSRVVPVKIGEPVKGAGRQYLVANAQLQD 300

Query: 300 FRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338
           +RAV+L+LD+APGKPV L +EAAEALGVGEGASVRLVAV
Sbjct: 301 YRAVLLELDYAPGKPVTLDLEAAEALGVGEGASVRLVAV 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: 450
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 Pf1N1B4_3442 (Arginine N-succinyltransferase, alpha subunit (EC 2.3.1.109))
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.6505.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.3e-171  555.3   0.0   3.7e-171  555.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3442  Arginine N-succinyltransferase, 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3442  Arginine N-succinyltransferase, alpha subunit (EC 2.3.1.109)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  555.2   0.0  3.7e-171  3.7e-171       1     336 []       3     339 .]       3     339 .] 0.99

  Alignments for each domain:
  == domain 1  score: 555.2 bits;  conditional E-value: 3.7e-171
                                      TIGR03245   1 vvrParladldaierlaresaigvtslPadrekleekiaqsessfaaevsfsgeesylfvleds 64 
                                                    v+rPa++adl +++rla++s+igvtslP+d e+l +kia+se sfaaevsf+geesy+fvled+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3442   3 VMRPAQMADLGEVQRLAADSPIGVTSLPDDVERLSDKIAASEASFAAEVSFNGEESYFFVLEDT 66 
                                                    79************************************************************** PP

                                      TIGR03245  65 etgkllGtasivasaGyaePfysyrndtlvhasrelkvnnkihvlslsheltGksllasfyvdp 128
                                                    +tgkl+G+++ivasaGy+ePfys+rn+t+vhasrelk++nkihvls +h+ltG+sll+sfyv+p
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3442  67 ATGKLVGCSAIVASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSQCHDLTGNSLLTSFYVKP 130
                                                    **************************************************************** PP

                                      TIGR03245 129 elreaeaaellsrarllfiaaererfasrviaellGvsdeaGesPfWdaiGrkffdldfaaver 192
                                                    el+++ +ael+sr+rllf+a+++erfa++v++e++G sde+G+sPfWdaiGr+ffdl++aa+er
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3442 131 ELVGSPWAELNSRGRLLFVASHPERFADSVVTEIVGYSDENGDSPFWDAIGRNFFDLNYAAAER 194
                                                    **************************************************************** PP

                                      TIGR03245 193 asglksktfiaelmPsyPiyvpllpdeaqealgqvheraelafdlllreGfeadryidifdgGp 256
                                                    ++glks+tf+aelmP+yPiyvpllpd+aqea+gqvh+ra+++fd+l+reGfe+d+yidifdgGp
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3442 195 LCGLKSRTFLAELMPHYPIYVPLLPDSAQEAMGQVHPRAQITFDILMREGFETDHYIDIFDGGP 258
                                                    **************************************************************** PP

                                      TIGR03245 257 vleaeldrlktvkksrekpvkieeaatgg.stylvsnglledfravladlavvdGkalrlkada 319
                                                    +l+a++++++++++sr++pvki e  +g  ++ylv+n +l+d+ravl++l+ ++Gk+++l+ +a
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3442 259 TLHARVSGIRSIAQSRVVPVKIGEPVKGAgRQYLVANAQLQDYRAVLLELDYAPGKPVTLDLEA 322
                                                    ************************999888********************************** PP

                                      TIGR03245 320 aealgvseGdavrlval 336
                                                    aealgv+eG++vrlva+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3442 323 AEALGVGEGASVRLVAV 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.23
//
[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