GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astA in Pseudomonas fluorescens FW300-N2C3

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate AO356_18735 AO356_18735 arginine N-succinyltransferase

Query= SwissProt::P0AE37
         (344 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 AO356_18735 arginine
           N-succinyltransferase
          Length = 341

 Score =  339 bits (870), Expect = 5e-98
 Identities = 173/342 (50%), 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   MIVRPVRSSDLPALIALARSTGTGLTTLPANEERLAHRVGWAEKTFRGEAGRGDADYLFV 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 +L+K+R +F+A F   F +K++AEMRG+ D++G SPFW+SLG+
Sbjct: 120 LCSLFLHADYRSGLNGRMLAKARLLFIAEFPQLFGNKIIAEMRGMSDDNGRSPFWESLGR 179

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

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

Query: 302 VVLVRTDPATERLILTAAQLDALKCHAGDRVRLVRLCAEEKT 343
           +       A   L++       L+ +AGD+VR V L A  ++
Sbjct: 299 ITAAPARFAAGTLVVDPLTAKRLQLNAGDQVRAVALSAARES 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: 363
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 AO356_18735 AO356_18735 (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.26019.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.3e-159  516.5   0.0   1.4e-159  516.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735  AO356_18735 arginine N-succinylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735  AO356_18735 arginine N-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.3   0.0  1.4e-159  1.4e-159       1     336 []       2     334 ..       2     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 516.3 bits;  conditional E-value: 1.4e-159
                                       TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledt 63 
                                                     ivrpv++sdl+al++la+++G+Glt+lpanee+l++r+ +aek+f+ge+ r++++ylfvled 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735   2 IVRPVRSSDLPALIALARSTGTGLTTLPANEERLAHRVGWAEKTFRGEAGRGDADYLFVLED- 63 
                                                     79************************************************************. PP

                                       TIGR03244  64 etgkvvGvsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfld 126
                                                     ++g+vvG+sai+ avGl+ep+yn+rvg +v+as+elniy++++tlfl+ndltg+selC+lfl+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735  64 DDGRVVGISAIAGAVGLREPWYNFRVGLTVSASQELNIYREIPTLFLANDLTGNSELCSLFLH 126
                                                     99************************************************************* PP

                                       TIGR03244 127 eeyrkelnGkllskarflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfska 189
                                                      +yr++lnG++l+kar+lf+aef+++f++kiiaemrG+sd++GrsPfWe+lg++ff+++fs+a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 127 ADYRSGLNGRMLAKARLLFIAEFPQLFGNKIIAEMRGMSDDNGRSPFWESLGRHFFKMEFSQA 189
                                                     *************************************************************** PP

                                       TIGR03244 190 dylsgiGkkafiaelmPkfPiyvdllskeaqdvigkvhektkPalalleseGlryqgyvdifd 252
                                                     dyl+g+G+kafiaelmPkfP+y+++ls+ a++vig+vh++t+Pal +l+seG+ yqgyvdifd
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 190 DYLTGVGNKAFIAELMPKFPLYTCFLSEGARAVIGQVHPDTEPALSMLKSEGFSYQGYVDIFD 252
                                                     *************************************************************** PP

                                       TIGR03244 253 aGptleaevakiravresklvevavaesaaedeaepylvanekledfrvvlvessldaeelvl 315
                                                     aGp++e+e+ kira+r+s+ +++a++++ +++  +p+l++n+k ed+r+++++++ +a++lv+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 253 AGPAVECETGKIRAIRDSQALVLAIGTPGDDA--TPFLIHNRKREDCRITAAPARFAAGTLVV 313
                                                     **************************998665..***************************** PP

                                       TIGR03244 316 saeeakalkveeGdkvrvval 336
                                                     ++ +ak+l++++Gd+vr val
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 314 DPLTAKRLQLNAGDQVRAVAL 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.21
//
[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 paper from 2022 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