Alignments for a candidate for astA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Pseudomonas fluorescens GW456-L13

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate PfGW456L13_1973 Arginine N-succinyltransferase (EC 2.3.1.109)

Query= SwissProt::P0AE37
         (344 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973
          Length = 341

 Score =  345 bits (884), Expect = 1e-99
 Identities = 175/342 (51%), Positives = 235/342 (68%), Gaps = 2/342 (0%)

Query: 2   MVIRPVERSDVSALMQLASKTGGGLTSLPANEATLSARIERAIKTWQGELPKSEQGYVFV 61
           M++RPV  SD+ AL+ LA  TG GLT+LPANE  L+ R+  A KT++GE  + +  Y+FV
Sbjct: 1   MIVRPVRSSDLPALIDLARSTGTGLTTLPANEERLAHRVGWAEKTFRGEAGRGDADYLFV 60

Query: 62  LEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSE 121
           LED + G V GI AI  AVGL +PWYN+RVG  V AS+ELN+Y  +PTLFL+ND TG+SE
Sbjct: 61  LEDDD-GRVVGISAIAGAVGLREPWYNFRVGLTVSASQELNIYREIPTLFLANDLTGNSE 119

Query: 122 LCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSLGK 181
           LC+LFL  D+R   NG +LSK+R +F+A F   F +K++AEMRGV DE G SPFW+SLG+
Sbjct: 120 LCSLFLHADYRSGLNGRMLSKARMLFIAEFPQLFGNKIIAEMRGVSDEAGRSPFWESLGR 179

Query: 182 RFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVLEK 241
            FF M+FS+AD+L G G KAFIAELMPK P+YT FLS +A++VIGQVHP T PA A+L+ 
Sbjct: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSPDARNVIGQVHPDTEPALAMLKS 239

Query: 242 EGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVEVAEGQPAQGDFPACLVANENYHHFR 301
           EGF Y+ Y+DIFD GP +EC+  ++RA+R S+ + +A G P   D    ++ N      R
Sbjct: 240 EGFSYQGYVDIFDAGPAIECETGKIRAVRDSQALVLAVGTPGD-DATPFIIHNRKREDCR 298

Query: 302 VVLVRTDPATERLILTAAQLDALKCHAGDRVRLVRLCAEEKT 343
           +       A   L++       L+ +AGD+VR V L A  ++
Sbjct: 299 ITAAPARLAAGTLVVDPLTAKRLQLNAGDQVRAVALSAARES 340


Lambda     K      H
   0.321    0.136    0.411 

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: 355
Number of extensions: 18
Number of successful extensions: 3
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: 341
Length adjustment: 29
Effective length of query: 315
Effective length of database: 312
Effective search space:    98280
Effective search space used:    98280
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 PfGW456L13_1973 (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.12387.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   8.6e-162  523.6   0.0   9.8e-162  523.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973  Arginine N-succinyltransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973  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 !  523.4   0.0  9.8e-162  9.8e-162       1     336 []       2     334 ..       2     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 523.4 bits;  conditional E-value: 9.8e-162
                                               TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeeg 55 
                                                             ivrpv++sdl+al++la+++G+Glt+lpanee+l++r+ +aek+f+ge+ r++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973   2 IVRPVRSSDLPALIDLARSTGTGLTTLPANEERLAHRVGWAEKTFRGEAGRGDAD 56 
                                                             79***************************************************** PP

                                               TIGR03244  56 ylfvledtetgkvvGvsaieaavGleepfynyrvgkvvhaskelniykkletlfl 110
                                                             ylfvled ++g+vvG+sai+ avGl+ep+yn+rvg +v+as+elniy++++tlfl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973  57 YLFVLED-DDGRVVGISAIAGAVGLREPWYNFRVGLTVSASQELNIYREIPTLFL 110
                                                             *******.99********************************************* PP

                                               TIGR03244 111 sndltgaselCtlfldeeyrkelnGkllskarflflaefkerfskkiiaemrGvs 165
                                                             +ndltg+selC+lfl+ +yr++lnG++lskar+lf+aef+++f++kiiaemrGvs
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973 111 ANDLTGNSELCSLFLHADYRSGLNGRMLSKARMLFIAEFPQLFGNKIIAEMRGVS 165
                                                             ******************************************************* PP

                                               TIGR03244 166 deeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPiyvdllskeaq 220
                                                             de GrsPfWe+lg++ff+++fs+adyl+g+G+kafiaelmPkfP+y+++ls +a+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973 166 DEAGRSPFWESLGRHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSPDAR 220
                                                             ******************************************************* PP

                                               TIGR03244 221 dvigkvhektkPalalleseGlryqgyvdifdaGptleaevakiravresklvev 275
                                                             +vig+vh++t+Pala+l+seG+ yqgyvdifdaGp++e+e+ kiravr+s+ +++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973 221 NVIGQVHPDTEPALAMLKSEGFSYQGYVDIFDAGPAIECETGKIRAVRDSQALVL 275
                                                             ******************************************************* PP

                                               TIGR03244 276 avaesaaedeaepylvanekledfrvvlvessldaeelvlsaeeakalkveeGdk 330
                                                             av+++ +++  +p++++n+k ed+r+++++++l+a++lv+++ +ak+l++++Gd+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973 276 AVGTPGDDA--TPFIIHNRKREDCRITAAPARLAAGTLVVDPLTAKRLQLNAGDQ 328
                                                             ***998665..******************************************** PP

                                               TIGR03244 331 vrvval 336
                                                             vr val
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1973 329 VRAVAL 334
                                                             ***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (336 nodes)
Target sequences:                          1  (341 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: 10.32
//
[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