GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Shewanella amazonensis SB2B

Align fused chorismate mutase/prephenate dehydrogenase (EC 5.4.99.5; EC 1.3.1.12) (characterized)
to candidate 6936707 Sama_0894 bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq)

Query= ecocyc::CHORISMUTPREPHENDEHYDROG-MONOMER
         (373 letters)



>FitnessBrowser__SB2B:6936707
          Length = 379

 Score =  427 bits (1098), Expect = e-124
 Identities = 216/371 (58%), Positives = 269/371 (72%), Gaps = 1/371 (0%)

Query: 3   AELTALRDQIDEVDKALLNLLAKRLELVAEVGEVKSRFGLPIYVPEREASMLASRRAEAE 62
           AEL  LR  ID VD  LL+LL KRL+LVA+VG VK   GLPIY P REA+ML  RRAEAE
Sbjct: 7   AELENLRGLIDGVDSQLLSLLRKRLDLVAQVGTVKHAAGLPIYAPAREAAMLGKRRAEAE 66

Query: 63  ALGVPPDLIEDVLRRVMRESYSSENDKGFKTLCPSLRPVVIVGGGGQMGRLFEKMLTLSG 122
           A+GV P LIED+LRR+MRESY SE D GFK + P L  +VI+GG GQ+GRLF +M  LSG
Sbjct: 67  AMGVSPQLIEDILRRLMRESYMSEKDVGFKQVNPELGHIVIIGGQGQLGRLFAQMFALSG 126

Query: 123 YQVRILEQHDWDRAADIVADAGMVIVSVPIHVTEQVIG-KLPPLPKDCILVDLASVKNGP 181
           Y+VR+L++ DWD A ++   AG+V+V+VPI  T  +I  +L  LP+ CIL DL SVK  P
Sbjct: 127 YEVRLLDKDDWDHADELFDGAGLVLVTVPIATTCSLIRERLDHLPEHCILADLTSVKGAP 186

Query: 182 LQAMLVAHDGPVLGLHPMFGPDSGSLAKQVVVWCDGRKPEAYQWFLEQIQVWGARLHRIS 241
           L+AML  H GPV+GLHPMFGPD GSLAKQVVV C GR PE YQW +EQI +WGARL    
Sbjct: 187 LKAMLETHKGPVVGLHPMFGPDVGSLAKQVVVVCHGRAPEKYQWLMEQIGIWGARLVEAD 246

Query: 242 AVEHDQNMAFIQALRHFATFAYGLHLAEENVQLEQLLALSSPIYRLELAMVGRLFAQDPQ 301
           A  HD+ M  +QA+RHF++F YGL+L  E   ++ LL  SSPIYRLELAMVGRLFAQ  +
Sbjct: 247 AGRHDKAMQLVQAMRHFSSFVYGLNLCREQADIDTLLEFSSPIYRLELAMVGRLFAQSGE 306

Query: 302 LYADIIMSSERNLALIKRYYKRFGEAIELLEQGDKQAFIDSFRKVEHWFGDYAQRFQSES 361
           LYADII + E +L  I  +   + +A+ELL+ GD+  FI  F +V +WFG+Y+Q+F +ES
Sbjct: 307 LYADIIFAQEESLTAISDFIDNYRDALELLKTGDRAGFIARFNEVSNWFGNYSQQFLTES 366

Query: 362 RVLLRQANDNR 372
           R +L+  ND R
Sbjct: 367 RAMLQSVNDMR 377


Lambda     K      H
   0.322    0.138    0.404 

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: 403
Number of extensions: 17
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: 373
Length of database: 379
Length adjustment: 30
Effective length of query: 343
Effective length of database: 349
Effective search space:   119707
Effective search space used:   119707
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: 50 (23.9 bits)

Align candidate 6936707 Sama_0894 (bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq))
to HMM TIGR01799 (tyrA: chorismate mutase (EC 5.4.99.5))

# 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.aa/TIGR01799.hmm
# target sequence database:        /tmp/gapView.15556.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01799  [M=83]
Accession:   TIGR01799
Description: CM_T: chorismate mutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.2e-47  146.2   0.8    2.7e-47  145.1   0.8    1.6  1  lcl|FitnessBrowser__SB2B:6936707  Sama_0894 bifunctional chorismat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936707  Sama_0894 bifunctional chorismate mutase/prephenate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.1   0.8   2.7e-47   2.7e-47       1      83 []       9      91 ..       9      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 2.7e-47
                         TIGR01799  1 lkdlrdeidevdkellqllakrlelvaqvGkvkhraGlPiyaPereaamlakrreeaeklGiapdliedvlrrlmresy 79
                                      l++lr+ id+vd +ll ll+krl+lvaqvG+vkh+aGlPiyaP reaaml krr+eae++G++p+lied+lrrlmresy
  lcl|FitnessBrowser__SB2B:6936707  9 LENLRGLIDGVDSQLLSLLRKRLDLVAQVGTVKHAAGLPIYAPAREAAMLGKRRAEAEAMGVSPQLIEDILRRLMRESY 87
                                      799**************************************************************************** PP

                         TIGR01799 80 anen 83
                                      ++e+
  lcl|FitnessBrowser__SB2B:6936707 88 MSEK 91
                                      **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (83 nodes)
Target sequences:                          1  (379 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.73
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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