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.27051.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.82
//
[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