Alignments for a candidate for cmutase in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Shewanella amazonensis SB2B

Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate 6936711 Sama_0898 prephenate dehydratase / chorismate mutase / phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= CharProtDB::CH_024084
         (386 letters)



>FitnessBrowser__SB2B:6936711
          Length = 659

 Score =  409 bits (1051), Expect = e-118
 Identities = 213/386 (55%), Positives = 275/386 (71%), Gaps = 7/386 (1%)

Query: 1   MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60
           M    PL   RE+I+ +D  +L LLA RREL++EV ++K +  RPVRD  RER+LL RL+
Sbjct: 1   MEKPQPLSETREQITDIDNTVLQLLARRRELSLEVARSKEVDVRPVRDTQRERELLSRLV 60

Query: 61  TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKINPHSAR----IAFLGPKGSYS 116
             G+   LD H++ +L+Q IIEDSVL QQA L     + NP + +    IA+LG +GSYS
Sbjct: 61  QKGREQGLDPHFVMQLYQSIIEDSVLNQQAYLH---GRANPETQKQQYCIAYLGARGSYS 117

Query: 117 HLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHT 176
           +LAA +Y  R     ++ GC  F +I + VE+G ADY  +PIENTSSG+IN+VYD+LQHT
Sbjct: 118 YLAANRYCQRRQVDMVDLGCQSFDEIVHAVESGHADYGFLPIENTSSGSINEVYDVLQHT 177

Query: 177 SLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSA 236
           SL+IVGE T+ + HCLL    T  S I T+Y+HPQP  QCS++L R+P  ++EY  S++ 
Sbjct: 178 SLAIVGETTIEVGHCLLAKPGTKASDIKTLYAHPQPISQCSRYLARHPGLRLEYCASSAE 237

Query: 237 AMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPA 296
           AMEKV  A S  VAA+GS  GG LY L+ +E+  ANQ+ N +RF+V+ARKA+ V +Q+PA
Sbjct: 238 AMEKVQAADSKDVAAIGSAEGGGLYQLEAIEKGLANQKVNQSRFIVVARKAVAVPEQLPA 297

Query: 297 KTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQ 356
           K TL+MATGQ+ GALVEALLVL+ +NL M++LESRPI G PWEEMFYLDI ANL S  MQ
Sbjct: 298 KCTLIMATGQKPGALVEALLVLKANNLNMSKLESRPIPGTPWEEMFYLDIDANLASVPMQ 357

Query: 357 KALKELGEITRSMKVLGCYPSENVVP 382
            ALKEL  ITR +KVLGCYP E V P
Sbjct: 358 LALKELERITRFIKVLGCYPCETVAP 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: 499
Number of extensions: 13
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: 659
Length adjustment: 34
Effective length of query: 352
Effective length of database: 625
Effective search space:   220000
Effective search space used:   220000
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 6936711 Sama_0898 (prephenate dehydratase / chorismate mutase / phospho-2-dehydro-3-deoxyheptonate aldolase (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.23148.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.1e-29   88.7   2.8      2e-29   87.9   2.8    1.5  1  lcl|FitnessBrowser__SB2B:6936711  Sama_0898 prephenate dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936711  Sama_0898 prephenate dehydratase / chorismate mutase / phospho-2-dehydro-3-deoxyhep
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   2.8     2e-29     2e-29       1      83 []       7      89 ..       7      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 2e-29
                         TIGR01797  1 llalrekisaidkkllkllaerkelafevakskllsqkavrdierekkllqklitlgkkyqleaeyitrlfqliiedsv 79
                                      l++ re+i++id+ +l+lla r+el +eva+sk+++ ++vrd +re++ll +l++ g++  l+ +++ +l+q iiedsv
  lcl|FitnessBrowser__SB2B:6936711  7 LSETREQITDIDNTVLQLLARRRELSLEVARSKEVDVRPVRDTQRERELLSRLVQKGREQGLDPHFVMQLYQSIIEDSV 85
                                      6789*************************************************************************** PP

                         TIGR01797 80 ltqq 83
                                      l qq
  lcl|FitnessBrowser__SB2B:6936711 86 LNQQ 89
                                      **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (83 nodes)
Target sequences:                          1  (659 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: 19.20
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis