Alignments for a candidate for hisF in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisF in Shewanella oneidensis MR-1

Align IGP synthase cyclase subunit; EC 4.1.3.- (characterized)
to candidate 201225 SO2068 hisF protein (cyclase) (NCBI ptt file)

Query= CharProtDB::CH_024847
         (258 letters)



>FitnessBrowser__MR1:201225
          Length = 257

 Score =  390 bits (1001), Expect = e-113
 Identities = 190/256 (74%), Positives = 219/256 (85%)

Query: 1   MLAKRIIPCLDVRDGQVVKGVQFRNHEIIGDIVPLAKRYAEEGADELVFYDITASSDGRV 60
           MLAKRI+PCLDV+DG VVKGVQFRNHEI+GDIVPLA RYA EGADELVFYDITAS+  RV
Sbjct: 1   MLAKRIVPCLDVKDGCVVKGVQFRNHEIVGDIVPLAARYAAEGADELVFYDITASAHDRV 60

Query: 61  VDKSWVSRVAEVIDIPFCVAGGIKSLEDAAKILSFGADKISINSPALADPTLITRLADRF 120
           VDKSWVSRVAE IDIPFCVAGGIK++  A ++L+FGADKIS+NSPAL+DP+LI+RL D F
Sbjct: 61  VDKSWVSRVAEQIDIPFCVAGGIKTITQARELLAFGADKISVNSPALSDPSLISRLQDEF 120

Query: 121 GVQCIVVGIDTWYDAETGKYHVNQYTGDESRTRVTQWETLDWVQEVQKRGAGEIVLNMMN 180
           G QCIV+GID++YDA +  Y V Q+TGDE+ T+ T W T DWV+EVQKRG GEIVLN+MN
Sbjct: 121 GRQCIVIGIDSFYDAASDSYKVKQFTGDEAATKETAWYTQDWVEEVQKRGCGEIVLNVMN 180

Query: 181 QDGVRNGYDLEQLKKVREVCHVPLIASGGAGTMEHFLEAFRDADVDGALAASVFHKQIIN 240
           QDGVR GYD++QL  VR++C VPLIASGGAGTM HF + F DA VD ALAASVFHK IIN
Sbjct: 181 QDGVRGGYDIKQLSLVRQLCDVPLIASGGAGTMAHFRDVFIDAKVDAALAASVFHKAIIN 240

Query: 241 IGELKAYLATQGVEIR 256
           IGELK YLA +G+ IR
Sbjct: 241 IGELKQYLAAEGIAIR 256


Lambda     K      H
   0.321    0.138    0.409 

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: 319
Number of extensions: 8
Number of successful extensions: 1
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: 258
Length of database: 257
Length adjustment: 24
Effective length of query: 234
Effective length of database: 233
Effective search space:    54522
Effective search space used:    54522
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate 201225 SO2068 (hisF protein (cyclase) (NCBI ptt file))
to HMM TIGR00735 (hisF: imidazoleglycerol phosphate synthase, cyclase subunit)

# 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/TIGR00735.hmm
# target sequence database:        /tmp/gapView.10426.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00735  [M=254]
Accession:   TIGR00735
Description: hisF: imidazoleglycerol phosphate synthase, cyclase subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-108  347.0   2.0     3e-108  346.9   2.0    1.0  1  lcl|FitnessBrowser__MR1:201225  SO2068 hisF protein (cyclase) (N


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201225  SO2068 hisF protein (cyclase) (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.9   2.0    3e-108    3e-108       1     254 []       1     256 [.       1     256 [. 0.98

  Alignments for each domain:
  == domain 1  score: 346.9 bits;  conditional E-value: 3e-108
                       TIGR00735   1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiPltv 79 
                                     mlakri+pCLdvkdg vvkGvqf+n++ +Gd+v+la++y++eGadelvf+ditas+++r +++++v+rvae+++iP++v
  lcl|FitnessBrowser__MR1:201225   1 MLAKRIVPCLDVKDGCVVKGVQFRNHEIVGDIVPLAARYAAEGADELVFYDITASAHDRVVDKSWVSRVAEQIDIPFCV 79 
                                     8****************************************************************************** PP

                       TIGR00735  80 gGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevtikgGres....td 154
                                     +GGik+i+++++ll++Gadk+s+n++a+ +p li++l d fG+q+iv++id+ ++a ++  +y+v++ +G+e     t 
  lcl|FitnessBrowser__MR1:201225  80 AGGIKTITQARELLAFGADKISVNSPALSDPSLISRLQDEFGRQCIVIGIDSFYDAASD--SYKVKQFTGDEAatkeTA 156
                                     ******************************************************99875..9********997666689 PP

                       TIGR00735 155 ldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkadaaLaasvfh 233
                                     + + +w++ev+++G Gei+l++m++dG++ Gyd+++l  v++ +++P+iasgGaG++ h++++f+++k+daaLaasvfh
  lcl|FitnessBrowser__MR1:201225 157 WYTQDWVEEVQKRGCGEIVLNVMNQDGVRGGYDIKQLSLVRQLCDVPLIASGGAGTMAHFRDVFIDAKVDAALAASVFH 235
                                     9999*************************************************************************** PP

                       TIGR00735 234 kreltieevkeylaergvkvr 254
                                     k +++i+e+k+yla++g+ +r
  lcl|FitnessBrowser__MR1:201225 236 KAIINIGELKQYLAAEGIAIR 256
                                     *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (257 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: 8.98
//
[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