Aligments for a candidate for cmutase in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Aligments for a candidate for cmutase in Shewanella oneidensis MR-1

Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate 200542 SO1367 chorismate mutase/prephenate dehydratase (NCBI ptt file)

Query= CharProtDB::CH_024084
         (386 letters)



>FitnessBrowser__MR1:200542
          Length = 671

 Score =  411 bits (1056), Expect = e-119
 Identities = 213/386 (55%), Positives = 277/386 (71%), Gaps = 7/386 (1%)

Query: 1   MTSENPLLALREKISALDEKLLALLAERRELAVEVGKAKLLSHRPVRDIDRERDLLERLI 60
           M    PL   RE+I+ LD  LL+LLAERR L++EV ++K +  RP+RD  RE++LL RL+
Sbjct: 1   MQKPQPLNHTREQITQLDNDLLSLLAERRRLSLEVARSKEVDVRPIRDTQREKELLARLV 60

Query: 61  TLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQHLNKINPHSAR----IAFLGPKGSYS 116
           T G+   LDAHY+  L+Q IIEDSVL QQA L     + NP + +    IA+LG +GSYS
Sbjct: 61  TAGREKGLDAHYVISLYQSIIEDSVLNQQAYLH---GRANPETQKQQYCIAYLGARGSYS 117

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

Query: 177 SLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSA 236
           SLSIVGE T+ + HCLL    + LS I TVY+HPQP  QCS++L+++   ++EY  S++ 
Sbjct: 178 SLSIVGETTIEVSHCLLGKPGSKLSEIKTVYAHPQPISQCSRYLSQHKALRLEYCSSSAE 237

Query: 237 AMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPA 296
           AMEKV Q+     AA+GS  GG LY L+ +E   ANQ+ N +RF+V+ARKA+ V +Q+PA
Sbjct: 238 AMEKVNQSPDNSAAAIGSAEGGALYQLESIESGLANQKINQSRFIVVARKAVAVPEQLPA 297

Query: 297 KTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYLDIQANLESAEMQ 356
           KTTL+MATGQ+AGALVEALLVL+ H L M++LESRPI G PWEEMFYLDI AN+ S  MQ
Sbjct: 298 KTTLIMATGQKAGALVEALLVLKAHQLNMSKLESRPIPGTPWEEMFYLDIDANISSEAMQ 357

Query: 357 KALKELGEITRSMKVLGCYPSENVVP 382
           + LK+L  ITR +KVLGCYP E V P
Sbjct: 358 QGLKQLERITRFIKVLGCYPCETVTP 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: 545
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: 671
Length adjustment: 34
Effective length of query: 352
Effective length of database: 637
Effective search space:   224224
Effective search space used:   224224
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 200542 SO1367 (chorismate mutase/prephenate dehydratase (NCBI ptt file))
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.21357.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    2.4e-32   97.2   2.6    5.1e-32   96.2   2.6    1.6  1  lcl|FitnessBrowser__MR1:200542  SO1367 chorismate mutase/prephen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200542  SO1367 chorismate mutase/prephenate dehydratase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   2.6   5.1e-32   5.1e-32       2      83 .]       8      89 ..       7      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 5.1e-32
                       TIGR01797  2 lalrekisaidkkllkllaerkelafevakskllsqkavrdierekkllqklitlgkkyqleaeyitrlfqliiedsvltq 82
                                       re+i+++d+ ll llaer++l +eva+sk+++ +++rd +rek+ll +l+t g++  l+a+y+ +l+q iiedsvl q
  lcl|FitnessBrowser__MR1:200542  8 NHTREQITQLDNDLLSLLAERRRLSLEVARSKEVDVRPIRDTQREKELLARLVTAGREKGLDAHYVISLYQSIIEDSVLNQ 88
                                    567*****************************************************************************9 PP

                       TIGR01797 83 q 83
                                    q
  lcl|FitnessBrowser__MR1:200542 89 Q 89
                                    8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (83 nodes)
Target sequences:                          1  (671 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: 15.58
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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:

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, or view the source code, or see 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