Alignments for a candidate for astA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Pseudomonas putida KT2440

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate PP_4479 PP_4479 arginine N-succinyltransferase, subunit beta

Query= SwissProt::P0AE37
         (344 letters)



>FitnessBrowser__Putida:PP_4479
          Length = 342

 Score =  330 bits (845), Expect = 4e-95
 Identities = 170/342 (49%), Positives = 230/342 (67%), Gaps = 3/342 (0%)

Query: 2   MVIRPVERSDVSALMQLASKTGG-GLTSLPANEATLSARIERAIKTWQGELPKSEQGYVF 60
           M++RPV  SD+ AL++LA  TG  GLT+LPANE  L  R+  A K+++GE  + +  Y+F
Sbjct: 1   MIVRPVRSSDLPALIELARSTGTTGLTTLPANEERLGHRVGWAEKSFRGEAERGDTDYLF 60

Query: 61  VLEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSS 120
           VLE+ E G V GI AI  AVGL +PWYNYRVG  V AS+EL +Y  +PTLFL+ND TG+S
Sbjct: 61  VLENDE-GLVVGISAIAGAVGLREPWYNYRVGLTVSASQELKIYREIPTLFLANDLTGNS 119

Query: 121 ELCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSLG 180
           ELC+LFL  D+R   NG LLS++R +F+A F + F  K++AEMRG+ DE G SPFW+SLG
Sbjct: 120 ELCSLFLRSDYRSGLNGRLLSRARMLFIAEFPELFGKKIIAEMRGMSDEQGRSPFWESLG 179

Query: 181 KRFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVLE 240
           + FF M+FS+AD+L G G K+FIAELMPK P+YT FLS+ A+ VIG+VH  T PA A+L+
Sbjct: 180 RHFFKMEFSQADYLTGVGNKSFIAELMPKFPLYTCFLSEAARSVIGRVHKDTEPALAMLK 239

Query: 241 KEGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVEVAEGQPAQGDFPACLVANENYHHF 300
           +EGF Y+ Y+DIFD GP +ECD  ++RA+R+S+ + +A G P   D    ++ N      
Sbjct: 240 QEGFNYQGYVDIFDAGPAIECDTAKIRAVRESQTLVLAVGTPGD-DATPFIIHNRKRDDC 298

Query: 301 RVVLVRTDPATERLILTAAQLDALKCHAGDRVRLVRLCAEEK 342
           R+       A   L++       L+   GD VR V L A  +
Sbjct: 299 RITAAPARLAAGTLVVDPLTAKRLRMGVGDNVRAVPLSASRE 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: 339
Number of extensions: 13
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: 342
Length adjustment: 29
Effective length of query: 315
Effective length of database: 313
Effective search space:    98595
Effective search space used:    98595
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 PP_4479 PP_4479 (arginine N-succinyltransferase, subunit beta)
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.32168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.5e-161  522.1   0.0   2.8e-161  521.9   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4479  PP_4479 arginine N-succinyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4479  PP_4479 arginine N-succinyltransferase, subunit beta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.9   0.0  2.8e-161  2.8e-161       1     336 []       2     335 ..       2     335 .. 0.99

  Alignments for each domain:
  == domain 1  score: 521.9 bits;  conditional E-value: 2.8e-161
                           TIGR03244   1 ivrpvktsdldallelakeaGv.GltslpaneellekrieraeksfageleraeegylfvledtetgkvvGvsai 74 
                                         ivrpv++sdl+al+ela+++G+ Glt+lpanee+l +r+ +aeksf+ge+er++++ylfvle+ ++g vvG+sai
  lcl|FitnessBrowser__Putida:PP_4479   2 IVRPVRSSDLPALIELARSTGTtGLTTLPANEERLGHRVGWAEKSFRGEAERGDTDYLFVLEN-DEGLVVGISAI 75 
                                         79*******************88***************************************9.99********* PP

                           TIGR03244  75 eaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrkelnGkllskarflflaef 149
                                         + avGl+ep+ynyrvg +v+as+el+iy++++tlfl+ndltg+selC+lfl+++yr++lnG+lls+ar+lf+aef
  lcl|FitnessBrowser__Putida:PP_4479  76 AGAVGLREPWYNYRVGLTVSASQELKIYREIPTLFLANDLTGNSELCSLFLRSDYRSGLNGRLLSRARMLFIAEF 150
                                         *************************************************************************** PP

                           TIGR03244 150 kerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPiyvdllskeaqdvig 224
                                         +e+f+kkiiaemrG+sde+GrsPfWe+lg++ff+++fs+adyl+g+G+k+fiaelmPkfP+y+++ls++a++vig
  lcl|FitnessBrowser__Putida:PP_4479 151 PELFGKKIIAEMRGMSDEQGRSPFWESLGRHFFKMEFSQADYLTGVGNKSFIAELMPKFPLYTCFLSEAARSVIG 225
                                         *************************************************************************** PP

                           TIGR03244 225 kvhektkPalalleseGlryqgyvdifdaGptleaevakiravresklvevavaesaaedeaepylvanekledf 299
                                         +vh++t+Pala+l++eG++yqgyvdifdaGp++e+++akiravres+++++av+++ +++  +p++++n+k +d+
  lcl|FitnessBrowser__Putida:PP_4479 226 RVHKDTEPALAMLKQEGFNYQGYVDIFDAGPAIECDTAKIRAVRESQTLVLAVGTPGDDA--TPFIIHNRKRDDC 298
                                         ******************************************************998665..************* PP

                           TIGR03244 300 rvvlvessldaeelvlsaeeakalkveeGdkvrvval 336
                                         r+++++++l+a++lv+++ +ak+l++  Gd+vr v+l
  lcl|FitnessBrowser__Putida:PP_4479 299 RITAAPARLAAGTLVVDPLTAKRLRMGVGDNVRAVPL 335
                                         **********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (336 nodes)
Target sequences:                          1  (342 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: 7.44
//
[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