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; AST; AOST; EC 2.3.1.109 (characterized)
to candidate Pf1N1B4_5857 Arginine N-succinyltransferase (EC 2.3.1.109)

Query= SwissProt::P0AE37
         (344 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5857
          Length = 344

 Score =  295 bits (756), Expect = 9e-85
 Identities = 153/343 (44%), Positives = 214/343 (62%), Gaps = 2/343 (0%)

Query: 2   MVIRPVERSDVSALMQLASKTGGGLTSLPANEATLSARIERAIKTWQGELPKSEQGYVFV 61
           M+IRPV+ +D+ AL+ L  + G G T+LPA+E  L+ R+  A +T+  ++ +++  Y+FV
Sbjct: 1   MIIRPVQVTDLPALLDLVQRAGPGFTTLPASEERLTHRVRWAQRTFAEQVERADADYLFV 60

Query: 62  LEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSE 121
           LED +   V G+ A+  AVGL +PWYNYRVG  V +S +L +   LPTLFL+N+ TG SE
Sbjct: 61  LEDDDQ-QVVGVSALVGAVGLREPWYNYRVGLTVSSSPDLGIARQLPTLFLNNEMTGQSE 119

Query: 122 LCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSLGK 181
           +C+LFL  D R   NG LLS  R +F+A F   F DK++AE+RG  DE G SPFW SLG+
Sbjct: 120 ICSLFLRHDQRHGNNGRLLSLGRLLFVAEFPHLFGDKLIAELRGSADEQGCSPFWDSLGR 179

Query: 182 RFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVLEK 241
            FF MDFS AD L G G KAFIAELMP+ P+YT  L+++AQ VIG+ HP T PA  +L  
Sbjct: 180 HFFKMDFSHADHLSGLGSKAFIAELMPRQPLYTCLLTEQAQAVIGKPHPNTEPALKILTA 239

Query: 242 EGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVEVAEGQPAQGDFPACLVANENYHHFR 301
           EGF ++ YIDIFD GP +E  + ++R +R S+ +E+A G       P  L+ N    + R
Sbjct: 240 EGFSHKGYIDIFDAGPVIEAPVSKIRTVRDSQRLELAIG-TLDDQAPIWLIHNRRLENCR 298

Query: 302 VVLVRTDPATERLILTAAQLDALKCHAGDRVRLVRLCAEEKTA 344
           +   +       LI+       L+   G+ VR V L   ++ A
Sbjct: 299 ITTAQARLVGNSLIVDRLTAKRLQLQPGNSVRAVPLRNRQQQA 341


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: 330
Number of extensions: 15
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 Pf1N1B4_5857 (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.17566.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.9e-138  446.9   0.0   2.2e-138  446.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5857  Arginine N-succinyltransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5857  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 !  446.7   0.0  2.2e-138  2.2e-138       1     336 []       2     334 ..       2     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 446.7 bits;  conditional E-value: 2.2e-138
                                      TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledte 64 
                                                    i+rpv+ +dl+all+l ++aG G+t+lpa ee+l++r+ +a+++fa+++era+++ylfvled +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5857   2 IIRPVQVTDLPALLDLVQRAGPGFTTLPASEERLTHRVRWAQRTFAEQVERADADYLFVLED-D 64 
                                                    79************************************************************.8 PP

                                      TIGR03244  65 tgkvvGvsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldee 128
                                                    +++vvGvsa+  avGl+ep+ynyrvg +v++s +l+i ++l+tlfl n++tg+se+C+lfl+++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5857  65 DQQVVGVSALVGAVGLREPWYNYRVGLTVSSSPDLGIARQLPTLFLNNEMTGQSEICSLFLRHD 128
                                                    999************************************************************* PP

                                      TIGR03244 129 yrkelnGkllskarflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadyl 192
                                                     r+++nG+lls  r+lf+aef+++f++k+iae+rG +de+G sPfW++lg++ff++dfs+ad+l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5857 129 QRHGNNGRLLSLGRLLFVAEFPHLFGDKLIAELRGSADEQGCSPFWDSLGRHFFKMDFSHADHL 192
                                                    **************************************************************** PP

                                      TIGR03244 193 sgiGkkafiaelmPkfPiyvdllskeaqdvigkvhektkPalalleseGlryqgyvdifdaGpt 256
                                                    sg+G+kafiaelmP+ P+y++ll+++aq+vigk h++t+Pal++l +eG+ ++gy+difdaGp+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5857 193 SGLGSKAFIAELMPRQPLYTCLLTEQAQAVIGKPHPNTEPALKILTAEGFSHKGYIDIFDAGPV 256
                                                    **************************************************************** PP

                                      TIGR03244 257 leaevakiravresklvevavaesaaedeaepylvanekledfrvvlvessldaeelvlsaeea 320
                                                    +ea v+kir+vr+s+++e+a+++  +  +a+  l++n++le++r+++++++l  ++l++++ +a
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5857 257 IEAPVSKIRTVRDSQRLELAIGTLDD--QAPIWLIHNRRLENCRITTAQARLVGNSLIVDRLTA 318
                                                    *********************97654..5699******************************** PP

                                      TIGR03244 321 kalkveeGdkvrvval 336
                                                    k+l+++ G++vr v+l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5857 319 KRLQLQPGNSVRAVPL 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.14
//
[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