Alignments for a candidate for astA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Pseudomonas fluorescens FW300-N2E2

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate Pf6N2E2_2181 Arginine N-succinyltransferase (EC 2.3.1.109)

Query= SwissProt::Q8ZPV1
         (344 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2181
          Length = 344

 Score =  310 bits (795), Expect = 3e-89
 Identities = 159/335 (47%), Positives = 217/335 (64%), Gaps = 2/335 (0%)

Query: 3   VIRPVEHADIAALMQLAGKTGGGLTSLPANEATLAARIERALKTWSGELPKGEQGYVFVL 62
           ++RPV   D+ AL+ LA   G G TSLPANE  LA RI  A +T++G++ + +  Y+FVL
Sbjct: 2   IVRPVAITDLPALLDLARCAGPGFTSLPANEERLAHRIRWAQRTFAGQVERADADYLFVL 61

Query: 63  EDSETGEVGGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSEL 122
           ED +  +V GI A+  AVGL +PWYNYRVG  V ++ EL +   +PTLFL+N+ +G SE+
Sbjct: 62  EDDDR-QVVGISALTGAVGLREPWYNYRVGLTVSSAPELGIQRQIPTLFLNNEMSGQSEI 120

Query: 123 CTLFLDPEWRKEGNGYLLSKSRFMFMAAFRDKFNEKVVAEMRGVIDEHGYSPFWQSLGKR 182
           C+LFL PE R+  NG LLS +R +F+A F   F EK++AE+RG  DE G SPFW SLG+ 
Sbjct: 121 CSLFLHPEQRRGHNGRLLSLARLLFVAEFSQLFGEKMIAELRGHADERGSSPFWDSLGRH 180

Query: 183 FFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSEEAQAVIGEVHPQTAPARAVLEKE 242
           FF  DFS AD L G G K+FIAELMP+ P+YT  L+E+AQAVIG+ HP T PA  +L  E
Sbjct: 181 FFKKDFSYADQLSGMGNKSFIAELMPRQPLYTCLLTEQAQAVIGKAHPNTEPALKILSAE 240

Query: 243 GFRYRHYIDIFDGGPTLECDIDRVRAIRKSRLVEVAEGQPAPGDYPACLVANENYHHFRA 302
           GF ++ YIDIFDGGP +E  + ++R +R S+++ +  G P P   P  L+ N    + R 
Sbjct: 241 GFSHKGYIDIFDGGPVIEAPVSKIRTVRDSQMLTLVIGTPDP-QAPVWLIHNRRLENCRV 299

Query: 303 ALVRADPQTSRLVLTAAQLDALKCRAGDHVRLVRL 337
              RA     +L++       L+ + GD VR V L
Sbjct: 300 TSARAHLHGHKLLVDRLTAKRLQVQPGDTVRAVAL 334


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: 319
Number of extensions: 11
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: 344
Length adjustment: 29
Effective length of query: 315
Effective length of database: 315
Effective search space:    99225
Effective search space used:    99225
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 Pf6N2E2_2181 (Arginine N-succinyltransferase (EC 2.3.1.109))
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.3837.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.9e-138  446.2   0.0   3.3e-138  446.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2181  Arginine N-succinyltransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2181  Arginine N-succinyltransferase (EC 2.3.1.109)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.1   0.0  3.3e-138  3.3e-138       1     336 []       2     334 ..       2     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 446.1 bits;  conditional E-value: 3.3e-138
                                      TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledte 64 
                                                    ivrpv  +dl+all+la+ aG G+tslpanee+l++ri +a+++fag++era+++ylfvled +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2181   2 IVRPVAITDLPALLDLARCAGPGFTSLPANEERLAHRIRWAQRTFAGQVERADADYLFVLED-D 64 
                                                    79************************************************************.8 PP

                                      TIGR03244  65 tgkvvGvsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldee 128
                                                    + +vvG+sa+  avGl+ep+ynyrvg +v+++ el+i ++++tlfl n++ g+se+C+lfl++e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2181  65 DRQVVGISALTGAVGLREPWYNYRVGLTVSSAPELGIQRQIPTLFLNNEMSGQSEICSLFLHPE 128
                                                    999************************************************************* PP

                                      TIGR03244 129 yrkelnGkllskarflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadyl 192
                                                     r+++nG+lls ar+lf+aef+++f++k+iae+rG++de G+sPfW++lg++ff+ dfs ad l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2181 129 QRRGHNGRLLSLARLLFVAEFSQLFGEKMIAELRGHADERGSSPFWDSLGRHFFKKDFSYADQL 192
                                                    **************************************************************** PP

                                      TIGR03244 193 sgiGkkafiaelmPkfPiyvdllskeaqdvigkvhektkPalalleseGlryqgyvdifdaGpt 256
                                                    sg+G+k+fiaelmP+ P+y++ll+++aq+vigk h++t+Pal++l +eG+ ++gy+difd+Gp+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2181 193 SGMGNKSFIAELMPRQPLYTCLLTEQAQAVIGKAHPNTEPALKILSAEGFSHKGYIDIFDGGPV 256
                                                    **************************************************************** PP

                                      TIGR03244 257 leaevakiravresklvevavaesaaedeaepylvanekledfrvvlvessldaeelvlsaeea 320
                                                    +ea v+kir+vr+s+++++ ++++  ++  +  l++n++le++rv+ ++++l+ ++l++++ +a
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2181 257 IEAPVSKIRTVRDSQMLTLVIGTPDPQA--PVWLIHNRRLENCRVTSARAHLHGHKLLVDRLTA 318
                                                    ***********************99988..99******************************** PP

                                      TIGR03244 321 kalkveeGdkvrvval 336
                                                    k+l+v+ Gd+vr val
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2181 319 KRLQVQPGDTVRAVAL 334
                                                    *************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (336 nodes)
Target sequences:                          1  (344 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: 7.46
//
[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