Alignments for a candidate for astA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Pseudomonas fluorescens FW300-N2E3

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate AO353_03015 AO353_03015 arginine N-succinyltransferase

Query= SwissProt::P0AE37
         (344 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03015
          Length = 341

 Score =  342 bits (878), Expect = 6e-99
 Identities = 174/342 (50%), Positives = 236/342 (69%), 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  LED-DNGRVVGISAIAGAVGLREPWYNFRVGLTVSASQELNIYREIPTLFLANDLTGNSE 119

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

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

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

Query: 302 VVLVRTDPATERLILTAAQLDALKCHAGDRVRLVRLCAEEKT 343
           +       A   L++       L+ +AGD+VR V L A  ++
Sbjct: 299 ITAAPARFAAGTLVVDPLTAKRLQLNAGDQVRAVPLSAARES 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: 356
Number of extensions: 19
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 AO353_03015 AO353_03015 (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.22895.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   3.1e-161  521.8   0.0   3.5e-161  521.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03015  AO353_03015 arginine N-succinylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03015  AO353_03015 arginine N-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.6   0.0  3.5e-161  3.5e-161       1     336 []       2     334 ..       2     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 521.6 bits;  conditional E-value: 3.5e-161
                                     TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledtet 65 
                                                   ivrpv++sdl+al++la+++G+Glt+lpanee+l++r+ +aek+f+ge+ r++++ylfvled ++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03015   2 IVRPVRSSDLPALIDLARSTGTGLTTLPANEERLAHRVGWAEKTFRGEAGRGDADYLFVLED-DN 65 
                                                   79************************************************************.99 PP

                                     TIGR03244  66 gkvvGvsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyr 130
                                                   g+vvG+sai+ avGl+ep+yn+rvg +v+as+elniy++++tlfl+ndltg+selC+lfl+ +yr
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03015  66 GRVVGISAIAGAVGLREPWYNFRVGLTVSASQELNIYREIPTLFLANDLTGNSELCSLFLHADYR 130
                                                   ***************************************************************** PP

                                     TIGR03244 131 kelnGkllskarflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgi 195
                                                   ++lnG++l+kar+lf+aef+++f++kiiaemrGvsde GrsPfWe+lg++ff+++fs+adyl+g+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03015 131 SGLNGRMLAKARMLFIAEFPQLFGNKIIAEMRGVSDEAGRSPFWESLGRHFFKMEFSQADYLTGV 195
                                                   ***************************************************************** PP

                                     TIGR03244 196 GkkafiaelmPkfPiyvdllskeaqdvigkvhektkPalalleseGlryqgyvdifdaGptleae 260
                                                   G+kafiaelmPkfP+y+++ls++a++vigkvh++t+Pala+l+seG+ yqgyvdifdaGp++e+e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03015 196 GNKAFIAELMPKFPLYTCFLSEDARNVIGKVHPDTEPALAMLKSEGFSYQGYVDIFDAGPAVECE 260
                                                   ***************************************************************** PP

                                     TIGR03244 261 vakiravresklvevavaesaaedeaepylvanekledfrvvlvessldaeelvlsaeeakalkv 325
                                                   + kiravr+s+ +++a++++ +++  +p+l++n+k ed+r+++++++ +a++lv+++ +ak+l++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03015 261 TGKIRAVRDSQALVLAIGTPGDDA--TPFLIHNRKREDCRITAAPARFAAGTLVVDPLTAKRLQL 323
                                                   ******************998665..*************************************** PP

                                     TIGR03244 326 eeGdkvrvval 336
                                                   ++Gd+vr v+l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03015 324 NAGDQVRAVPL 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.08
//
[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