Alignments for a candidate for cmutase in Desulfovibrio bastinii DSM 16055

GapMind for Amino acid biosynthesis

Alignments for a candidate for cmutase in Desulfovibrio bastinii DSM 16055

Align chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_027177480.1 G496_RS0100125 cytochrome c4

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



>NCBI__GCF_000429985.1:WP_027177480.1
          Length = 363

 Score =  355 bits (912), Expect = e-103
 Identities = 176/360 (48%), Positives = 247/360 (68%), Gaps = 1/360 (0%)

Query: 1   MKLNLNIQSLNTWLNVNNEPLIISGPCSAETEEQLLTTAHLLAATGKVSVLRAGIWKPRT 60
           M ++L+I  +  W    + PLII+GPCSAE+ EQ+L TA  +A +G   +LRAGIWKPRT
Sbjct: 1   MSVDLDITPIKDWGFEFDGPLIIAGPCSAESREQVLETAKGVAKSG-AHMLRAGIWKPRT 59

Query: 61  RPGEFEGIGSIGLEWLKRAKAETGLPTAVEVANAKHVEEALAAGVDILWIGARSTVNPFT 120
           RP  FEG+G  GL+WL  A+  TG+P +VE AN +HVE  L   VD++W+GAR+TVNPF 
Sbjct: 60  RPNCFEGMGEEGLKWLVEAREVTGMPISVETANPEHVELCLKYNVDLIWVGARTTVNPFA 119

Query: 121 VQEIADALKGHDVPVLIKNPVNPDLQLWIGAIERINGAGITKIGAIHRGFSSFEKSSFRN 180
           VQ +AD+L+G D+PVL+KNP+NPD++LWIGA+ER+N AG+TK+GAIHRGFSS   + +RN
Sbjct: 120 VQALADSLEGSDIPVLVKNPINPDVELWIGALERLNKAGVTKLGAIHRGFSSARATEYRN 179

Query: 181 EPMWELAIQLKTLCPELPIINDPSHICGNRELIPYISQKALDLDMQGLMIESHVDPSVAW 240
            P W + I+L+  C  +PII DPSH+CG R LIP ++QKALDL   GLMIESH++P VA 
Sbjct: 180 APNWRIFIELRRRCEGMPIICDPSHLCGKRALIPAVAQKALDLLFDGLMIESHINPDVAL 239

Query: 241 TDAKQQVTPAALAELVDRLTVREPEAPNEAFADKLADLRKSIDKIDDVLLQKLGERMAIV 300
           +D+KQQ TP  LA+++  L  R P A +E F   +   R  + +IDD ++  L ERM + 
Sbjct: 240 SDSKQQFTPDDLAKVIADLKPRNPAATDENFILSIEKERIRLGEIDDQIVDLLDERMQLS 299

Query: 301 EKIGEFKRDNQVTILQVNRWDAIIKKGHAFAKALKLDLNFTEKFLELVHGESIRKQTEIM 360
             IGE KR   + +LQ  +W    ++    A+   +D +F  +  + +H ES+R+Q +I+
Sbjct: 300 RHIGELKRSRGLALLQPAQWKKTAERRVEEAEKRGMDAHFMLRVFQYIHEESLRQQEDII 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: 376
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: 363
Length adjustment: 30
Effective length of query: 349
Effective length of database: 333
Effective search space:   116217
Effective search space used:   116217
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: 49 (23.5 bits)

Align candidate WP_027177480.1 G496_RS0100125 (cytochrome c4)
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.9928.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    8.5e-24   70.1   2.8    1.9e-23   69.0   2.8    1.6  1  lcl|NCBI__GCF_000429985.1:WP_027177480.1  G496_RS0100125 cytochrome c4


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429985.1:WP_027177480.1  G496_RS0100125 cytochrome c4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   2.8   1.9e-23   1.9e-23       1      79 []     278     356 ..     278     356 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 1.9e-23
                                      CM_2   1 RkeIdeiDrelleLlaeRmelakeiaeyKkenglpvldpeReeevlerlregaeelgldpeavekifre 69 
                                               R ++ eiD+++++Ll eRm+l++ i+e+K+++gl+ l+p+++++  er+ e+ae++g+d++++ ++f+ 
  lcl|NCBI__GCF_000429985.1:WP_027177480.1 278 RIRLGEIDDQIVDLLDERMQLSRHIGELKRSRGLALLQPAQWKKTAERRVEEAEKRGMDAHFMLRVFQY 346
                                               567889*************************************************************** PP

                                      CM_2  70 iisesralQk 79 
                                               i++es+++Q+
  lcl|NCBI__GCF_000429985.1:WP_027177480.1 347 IHEESLRQQE 356
                                               *******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (79 nodes)
Target sequences:                          1  (363 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: 12.44
//
[ok]

This GapMind analysis is from Apr 10 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