GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astA in Burkholderia phytofirmans PsJN

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate BPHYT_RS07705 BPHYT_RS07705 arginine succinyltransferase

Query= SwissProt::P0AE37
         (344 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS07705 BPHYT_RS07705 arginine
           succinyltransferase
          Length = 346

 Score =  320 bits (819), Expect = 4e-92
 Identities = 162/341 (47%), Positives = 227/341 (66%), Gaps = 8/341 (2%)

Query: 1   MMVIRPVERSDVSALMQLASKTGGGLTSLPANEATLSARIERAIKTWQGELPKSEQGYVF 60
           M+V+R V+R DV ALM+LA +TG GLT+   +   L+AR+ERA +T + +    E GY F
Sbjct: 1   MIVVRVVQRGDVDALMRLAQETGPGLTTFKPDRDALAARVERARRTMEDKAEAHEAGYFF 60

Query: 61  VLEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSS 120
           V+ED++TG VAG+C IE AVGL  P+YNYRV T+VHAS++L ++  +  L +S+D TG +
Sbjct: 61  VMEDTDTGDVAGVCGIETAVGLQQPFYNYRVSTVVHASQDLGIWTRMRALNISHDLTGYA 120

Query: 121 ELCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSLG 180
           E+C+LFL P +R  G G LLS+SRFMF+A FR++F  ++ AE+RG  D  G SPFW+++G
Sbjct: 121 EVCSLFLSPRYRTSGVGGLLSRSRFMFLAQFRERFPQRLCAELRGHFDAEGTSPFWRAVG 180

Query: 181 KRFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVLE 240
             F+ +DF+ AD+L   G+KAF+AELMP++P+Y   L +EAQ  +G  H  T PAR +LE
Sbjct: 181 SHFYQIDFNAADYLSSHGRKAFLAELMPRYPVYVELLPEEAQQCVGLTHNDTIPARRMLE 240

Query: 241 KEGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVEV------AEGQPAQGDFPACLVAN 294
            EG RY N++DIFD GP LEC I  +R +R+S +V V      A G P  G  P  +V+N
Sbjct: 241 SEGLRYENHVDIFDAGPVLECHIADLRTVRESVVVPVEIAPSSASGAPQDG--PKSMVSN 298

Query: 295 ENYHHFRVVLVRTDPATERLILTAAQLDALKCHAGDRVRLV 335
            +   FRV +V   P      L+A +  AL   AGD VR++
Sbjct: 299 TSLGDFRVGVVAGVPQDGVFRLSATEAAALDVKAGDLVRVL 339


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: 348
Number of extensions: 8
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: 346
Length adjustment: 29
Effective length of query: 315
Effective length of database: 317
Effective search space:    99855
Effective search space used:    99855
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 BPHYT_RS07705 BPHYT_RS07705 (arginine 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.6290.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   4.7e-150  485.0   0.0   5.5e-150  484.8   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07705  BPHYT_RS07705 arginine succinylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07705  BPHYT_RS07705 arginine succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.8   0.0  5.5e-150  5.5e-150       1     335 [.       3     340 ..       3     341 .. 0.98

  Alignments for each domain:
  == domain 1  score: 484.8 bits;  conditional E-value: 5.5e-150
                                TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledtetgkvvG 70 
                                              +vr+v++ d+dal++la+e+G Glt+++ ++++l++r+era++++++++e+ e+gy+fv+edt+tg+v+G
  lcl|FitnessBrowser__BFirm:BPHYT_RS07705   3 VVRVVQRGDVDALMRLAQETGPGLTTFKPDRDALAARVERARRTMEDKAEAHEAGYFFVMEDTDTGDVAG 72 
                                              79******************************************************************** PP

                                TIGR03244  71 vsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrkelnGkllsk 140
                                              v++ie+avGl++pfynyrv++vvhas++l+i++++ +l++s+dltg++e+C+lfl+++yr++ +G lls+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07705  73 VCGIETAVGLQQPFYNYRVSTVVHASQDLGIWTRMRALNISHDLTGYAEVCSLFLSPRYRTSGVGGLLSR 142
                                              ********************************************************************** PP

                                TIGR03244 141 arflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPi 210
                                              +rf+fla+f+erf ++++ae+rG++d eG+sPfW+a+g++f+++df++adyls++G+kaf+aelmP++P+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07705 143 SRFMFLAQFRERFPQRLCAELRGHFDAEGTSPFWRAVGSHFYQIDFNAADYLSSHGRKAFLAELMPRYPV 212
                                              ********************************************************************** PP

                                TIGR03244 211 yvdllskeaqdvigkvhektkPalalleseGlryqgyvdifdaGptleaevakiravresklvevavaes 280
                                              yv+ll++eaq+ +g +h++t Pa+++leseGlry+++vdifdaGp+le+++a++r+vres +v+v++a s
  lcl|FitnessBrowser__BFirm:BPHYT_RS07705 213 YVELLPEEAQQCVGLTHNDTIPARRMLESEGLRYENHVDIFDAGPVLECHIADLRTVRESVVVPVEIAPS 282
                                              *****************************************************************99765 PP

                                TIGR03244 281 a...aedeaepylvanekledfrvvlvessldaeelvlsaeeakalkveeGdkvrvva 335
                                              +   a +++++++v+n++l dfrv +v    + + + lsa+ea+al v++Gd vrv++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07705 283 SasgAPQDGPKSMVSNTSLGDFRVGVVAGVPQDGVFRLSATEAAALDVKAGDLVRVLP 340
                                              4111556799**********************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (336 nodes)
Target sequences:                          1  (346 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: 8.88
//
[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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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