GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_18735
          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.9806.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.20
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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