GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Shewanella loihica PV-4

Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate 5208561 Shew_1072 chorismate mutase (RefSeq)

Query= CharProtDB::CH_024084
         (386 letters)



>FitnessBrowser__PV4:5208561
          Length = 654

 Score =  416 bits (1070), Expect = e-121
 Identities = 213/383 (55%), Positives = 280/383 (73%), Gaps = 1/383 (0%)

Query: 1   MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60
           MT  +PL   RE+I+ALD +LLALLA+RR L+++V ++K +  RP+RD  RE++LL RL+
Sbjct: 1   MTKPHPLSHTREQITALDNELLALLAKRRALSLDVARSKEVDIRPIRDTQREKELLARLV 60

Query: 61  TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNK-INPHSARIAFLGPKGSYSHLA 119
             G+   LDAHY+  L+Q IIEDSVL QQA LQ   N  +      IA+LG +GSYS+LA
Sbjct: 61  KQGREQGLDAHYVLSLYQSIIEDSVLNQQAYLQGRANPDLQKQQYNIAYLGARGSYSYLA 120

Query: 120 ARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHTSLS 179
           A +Y  R      + GC  F +I   VE+G ADY  +PIENTSSG+IN+VYD+LQHTSL+
Sbjct: 121 ATRYCERRQVGMQDLGCKSFDEIVQAVESGHADYGFLPIENTSSGSINEVYDVLQHTSLA 180

Query: 180 IVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSAAME 239
           IVGE T+ + HCLL    T++  I T+Y+HPQP  QCS++L+++  +K+EY  S++ AME
Sbjct: 181 IVGETTIEVGHCLLAKPGTNVKQIKTIYAHPQPISQCSRYLSQHGEFKLEYCSSSAEAME 240

Query: 240 KVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPAKTT 299
           +V +A    VAA+GS  GG LY L+ +E   ANQ+ N +RF+V+ARKAI V +Q+PAKTT
Sbjct: 241 RVLEADDNSVAAIGSVEGGALYQLEAVEHELANQKINQSRFIVVARKAIAVPEQLPAKTT 300

Query: 300 LLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQKAL 359
           L+MATGQ+ GALVEALL+L+ H+L M++LESRPI G PWEEMFYLD+ ANL S EMQ+AL
Sbjct: 301 LIMATGQKPGALVEALLILKAHDLNMSKLESRPIPGTPWEEMFYLDLDANLASDEMQQAL 360

Query: 360 KELGEITRSMKVLGCYPSENVVP 382
           KEL  ITR +KVLGCYP E V P
Sbjct: 361 KELERITRFIKVLGCYPCETVNP 383


Lambda     K      H
   0.318    0.132    0.374 

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: 534
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: 386
Length of database: 654
Length adjustment: 34
Effective length of query: 352
Effective length of database: 620
Effective search space:   218240
Effective search space used:   218240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate 5208561 Shew_1072 (chorismate mutase (RefSeq))
to HMM TIGR01797 (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/TIGR01797.hmm
# target sequence database:        /tmp/gapView.20105.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01797  [M=83]
Accession:   TIGR01797
Description: CM_P_1: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    7.6e-31   92.4   2.9    2.1e-30   91.0   2.9    1.8  1  lcl|FitnessBrowser__PV4:5208561  Shew_1072 chorismate mutase (Ref


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208561  Shew_1072 chorismate mutase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   2.9   2.1e-30   2.1e-30       1      83 []       7      89 ..       7      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 2.1e-30
                        TIGR01797  1 llalrekisaidkkllkllaerkelafevakskllsqkavrdierekkllqklitlgkkyqleaeyitrlfqliiedsvl 80
                                     l+  re+i+a+d++ll+lla r+ l ++va+sk+++ +++rd +rek+ll +l++ g++  l+a+y+ +l+q iiedsvl
  lcl|FitnessBrowser__PV4:5208561  7 LSHTREQITALDNELLALLAKRRALSLDVARSKEVDIRPIRDTQREKELLARLVKQGREQGLDAHYVLSLYQSIIEDSVL 86
                                     6789**************************************************************************** PP

                        TIGR01797 81 tqq 83
                                      qq
  lcl|FitnessBrowser__PV4:5208561 87 NQQ 89
                                     *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (83 nodes)
Target sequences:                          1  (654 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: 21.89
//
[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