Alignments for a candidate for astA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Pseudomonas fluorescens FW300-N2C3

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate AO356_01530 AO356_01530 arginine N-succinyltransferase

Query= SwissProt::Q8ZPV1
         (344 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_01530
          Length = 344

 Score =  307 bits (787), Expect = 2e-88
 Identities = 159/335 (47%), Positives = 216/335 (64%), Gaps = 2/335 (0%)

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

Query: 63  EDSETGEVGGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSEL 122
           ED +  +V GI A+  AVGL +PWYNYRVG  V ++ EL +   +PTLFL+N+ +G SE+
Sbjct: 62  EDDDR-QVVGISALTGAVGLREPWYNYRVGVTVSSAPELGIQRQIPTLFLNNEMSGQSEI 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 CSLFLHPEQRHGHNGRLLSLARLLFVAEFSQLFGEKLIAELRGHADEQGCSPFWDSLGRH 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 FFQKDFSYADQLSGMGNKSFIAELMPRQPLYTCLLTEQAQAVIGKAHPNTEPALKILSAE 240

Query: 243 GFRYRHYIDIFDGGPTLECDIDRVRAIRKSRLVEVAEGQPAPGDYPACLVANENYHHFRA 302
           GF +R YIDIFDGGP +E  + ++R++R S+ + +A G P     P  L+ N    + R 
Sbjct: 241 GFSHRGYIDIFDGGPVIEAPVSKIRSVRDSQTLTLAIGTP-DEQAPVWLIHNRRLENCRV 299

Query: 303 ALVRADPQTSRLVLTAAQLDALKCRAGDHVRLVRL 337
              RA    + L++       L+ + GD VR V L
Sbjct: 300 TSARARLHGNSLLVDRLTAKRLQVQPGDTVRAVAL 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: 316
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 AO356_01530 AO356_01530 (arginine N-succinyltransferase)
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.26894.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     2e-139  450.0   0.0   2.3e-139  449.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01530  AO356_01530 arginine N-succinylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01530  AO356_01530 arginine N-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.9   0.0  2.3e-139  2.3e-139       1     336 []       2     334 ..       2     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 449.9 bits;  conditional E-value: 2.3e-139
                                       TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledt 63 
                                                     ivrpv  +dl+all+la+ aG G+tslpanee+l++r+ +a+++fag++era+++ylfvled 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01530   2 IVRPVALTDLPALLDLARCAGPGFTSLPANEERLAHRVRWAQRTFAGQVERADADYLFVLED- 63 
                                                     79************************************************************. PP

                                       TIGR03244  64 etgkvvGvsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfld 126
                                                     ++ +vvG+sa+  avGl+ep+ynyrvg +v+++ el+i ++++tlfl n++ g+se+C+lfl+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01530  64 DDRQVVGISALTGAVGLREPWYNYRVGVTVSSAPELGIQRQIPTLFLNNEMSGQSEICSLFLH 126
                                                     8999*********************************************************** PP

                                       TIGR03244 127 eeyrkelnGkllskarflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfska 189
                                                     +e r+++nG+lls ar+lf+aef+++f++k+iae+rG++de+G sPfW++lg++ff+ dfs a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01530 127 PEQRHGHNGRLLSLARLLFVAEFSQLFGEKLIAELRGHADEQGCSPFWDSLGRHFFQKDFSYA 189
                                                     *************************************************************** PP

                                       TIGR03244 190 dylsgiGkkafiaelmPkfPiyvdllskeaqdvigkvhektkPalalleseGlryqgyvdifd 252
                                                     d lsg+G+k+fiaelmP+ P+y++ll+++aq+vigk h++t+Pal++l +eG+ ++gy+difd
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01530 190 DQLSGMGNKSFIAELMPRQPLYTCLLTEQAQAVIGKAHPNTEPALKILSAEGFSHRGYIDIFD 252
                                                     *************************************************************** PP

                                       TIGR03244 253 aGptleaevakiravresklvevavaesaaedeaepylvanekledfrvvlvessldaeelvl 315
                                                     +Gp++ea v+kir+vr+s+++++a++++ +++  +  l++n++le++rv+ ++++l+ ++l++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01530 253 GGPVIEAPVSKIRSVRDSQTLTLAIGTPDEQA--PVWLIHNRRLENCRVTSARARLHGNSLLV 313
                                                     **************************998777..99*************************** PP

                                       TIGR03244 316 saeeakalkveeGdkvrvval 336
                                                     ++ +ak+l+v+ Gd+vr val
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01530 314 DRLTAKRLQVQPGDTVRAVAL 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.06
//
[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