Alignments for a candidate for cmutase in Thermophagus xiamenensis HS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Thermophagus xiamenensis HS1

Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_010528794.1 GQW_RS0115590 chorismate mutase

Query= reanno::Pedo557:CA265_RS11635
         (379 letters)



>NCBI__GCF_000220155.1:WP_010528794.1
          Length = 369

 Score =  404 bits (1037), Expect = e-117
 Identities = 197/342 (57%), Positives = 254/342 (74%), Gaps = 1/342 (0%)

Query: 20  PLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRTRPGEFEGIGSIGLEWLKRA 79
           P+IISGPCSAETEEQ L TA  L+A G + + RAGIWKPRTRPG FEG+G++GL WLKR 
Sbjct: 19  PIIISGPCSAETEEQTLNTAKELSARG-IKIFRAGIWKPRTRPGAFEGVGTVGLPWLKRV 77

Query: 80  KAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFTVQEIADALKGHDVPVLIKN 139
           K ETG+   VEVA + HV EA+  GVD++WIGAR++ NPF VQEIADALKG D+PV++KN
Sbjct: 78  KEETGMFICVEVATSHHVYEAVKFGVDMVWIGARTSANPFAVQEIADALKGLDMPVMVKN 137

Query: 140 PVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRNEPMWELAIQLKTLCPELPI 199
           PVNPDL+LWIGA+ER+N AGIT++ AIHRGFSS+++S FRN P W++ I+L+   PELPI
Sbjct: 138 PVNPDLELWIGALERLNRAGITRLAAIHRGFSSYDQSEFRNNPQWQIPIELRRRIPELPI 197

Query: 200 INDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAWTDAKQQVTPAALAELVDRL 259
           I DPSHI GNREL+  I+Q+A+DL+  GL+IESH+ P  AW+DAKQQVTP  L E++D L
Sbjct: 198 ITDPSHIGGNRELLAGIAQEAMDLNFDGLIIESHICPDKAWSDAKQQVTPEMLKEILDNL 257

Query: 260 TVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIVEKIGEFKRDNQVTILQVNR 319
            +R P+   +     L +LRK ID++DD LL  L ERM I E IG++K +N +TILQ  R
Sbjct: 258 VLRRPKIGEDTPRVTLDELRKQIDQLDDQLLDLLKERMKISEAIGKYKFENNITILQTRR 317

Query: 320 WDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIMN 361
           +D ++           L+ +F  K  E +H ESI +Q+EIMN
Sbjct: 318 YDEVLNNRRERGSQRGLNEDFITKIFESIHEESINRQSEIMN 359


Lambda     K      H
   0.317    0.134    0.389 

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: 414
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: 379
Length of database: 369
Length adjustment: 30
Effective length of query: 349
Effective length of database: 339
Effective search space:   118311
Effective search space used:   118311
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_010528794.1 GQW_RS0115590 (chorismate mutase)
to HMM PF01817 (CM_2)

# 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/PF01817.25.hmm
# target sequence database:        /tmp/gapView.1477771.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       CM_2  [M=79]
Accession:   PF01817.25
Description: Chorismate mutase type II
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.5e-28   85.4   4.7      2e-28   85.0   3.7    1.8  2  NCBI__GCF_000220155.1:WP_010528794.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000220155.1:WP_010528794.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         1         1      57      69 ..     244     256 ..     239     258 .. 0.55
   2 !   85.0   3.7     2e-28     2e-28       1      78 [.     277     354 ..     277     355 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1
                                  CM_2  57 gldpeavekifre 69 
                                           ++ pe++++i+++
  NCBI__GCF_000220155.1:WP_010528794.1 244 QVTPEMLKEILDN 256
                                           4556666665544 PP

  == domain 2  score: 85.0 bits;  conditional E-value: 2e-28
                                  CM_2   1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlregaeelgldpeavekifreiise 73 
                                           Rk+Id++D++ll+Ll+eRm+++++i++yK en++++l++ R +evl+++re  +++gl++++++kif+ i++e
  NCBI__GCF_000220155.1:WP_010528794.1 277 RKQIDQLDDQLLDLLKERMKISEAIGKYKFENNITILQTRRYDEVLNNRRERGSQRGLNEDFITKIFESIHEE 349
                                           9**************************************************999******************* PP

                                  CM_2  74 sralQ 78 
                                           s+++Q
  NCBI__GCF_000220155.1:WP_010528794.1 350 SINRQ 354
                                           ***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (79 nodes)
Target sequences:                          1  (369 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: 15.17
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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