Alignments for a candidate for tpi in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Marinobacter adhaerens HP15

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF2201 HP15_2155 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__Marino:GFF2201
          Length = 268

 Score =  209 bits (531), Expect = 6e-59
 Identities = 112/258 (43%), Positives = 161/258 (62%), Gaps = 6/258 (2%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCA-VAIAPPEMYIDMAKREAEGSHI 59
           MR P+++GNWK+NGS      L+  +   L        + + PP  Y+   +     + I
Sbjct: 1   MRKPILIGNWKMNGSLQANQALMVRVLPRLRMFRKSVDLVVCPPHPYLFQVRDLLGYTGI 60

Query: 60  MLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119
           MLGAQN    +SGA+TGE SA ML+++G +Y ++GHSERR    E ++ +A ++  + + 
Sbjct: 61  MLGAQNASGFVSGAYTGEVSATMLQEMGCRYALVGHSERRLLFGEGNQEVAARYRSVLQS 120

Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179
           GLTPVLC+GET  + E+G+T  +  +Q+ AV+   G AA    ++AYEPVWAIGTGK+AT
Sbjct: 121 GLTPVLCVGETLEDRESGRTGLIIEQQLQAVIDEVGLAAMANGIVAYEPVWAIGTGKTAT 180

Query: 180 PAQAQAVHKFIRDHIAKVDA----NIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGA 235
           P Q   VH+ IR  +AK       +I+E++ + YGGSV  +NA ELF+  D+DG L+GGA
Sbjct: 181 PEQVSEVHQQIRQFLAKSAPESADDISEELRVIYGGSVKVANAYELFSLADVDGGLIGGA 240

Query: 236 SLKADAFAVIVKA-AEAA 252
           SL AD F  I  A AEA+
Sbjct: 241 SLHADEFGTIAGALAEAS 258


Lambda     K      H
   0.316    0.130    0.366 

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: 190
Number of extensions: 5
Number of successful extensions: 3
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: 255
Length of database: 268
Length adjustment: 25
Effective length of query: 230
Effective length of database: 243
Effective search space:    55890
Effective search space used:    55890
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: 47 (22.7 bits)

Align candidate GFF2201 HP15_2155 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# 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.carbon/TIGR00419.hmm
# target sequence database:        /tmp/gapView.1040037.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.9e-62  197.1   0.0    2.2e-62  196.8   0.0    1.0  1  FitnessBrowser__Marino:GFF2201  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Marino:GFF2201  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.8   0.0   2.2e-62   2.2e-62       1     228 []       5     245 ..       5     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 196.8 bits;  conditional E-value: 2.2e-62
                       TIGR00419   1 lviinfKlnesvgkvelevaklaeev.aseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGeisAem 77 
                                     ++i+n+K+n+s++  + ++ ++   +   ++ v ++v pp+ +l  v+d +  + i+++Aqn     sGa+tGe+sA m
  FitnessBrowser__Marino:GFF2201   5 ILIGNWKMNGSLQANQALMVRVLPRLrMFRKSVDLVVCPPHPYLFQVRDLLGyTGIMLGAQNASGFVSGAYTGEVSATM 83 
                                     579********987776666666655156899*******************9999************************ PP

                       TIGR00419  78 lkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnvattaaaaAlep 149
                                     l+++G+++ l+gHsErR l+ e ++ ++++   + + gl++v+Cvgetle+re         +++++v ++ + aA+ +
  FitnessBrowser__Marino:GFF2201  84 LQEMGCRYALVGHSERRLLFGEGNQEVAARYRSVLQSGLTPVLCVGETLEDREsgrtgliIEQQLQAVIDEVGLAAMAN 162
                                     *****************************************************88888888889*************** PP

                       TIGR00419 150 dvvAvEPveliGtGkpvskAeaevveksvrdhlkk....vskevaesvrvlyGasvtaaedaelaaqldvdGvLlasav 224
                                      +vA+EPv++iGtGk++++ +  +v++++r++l+k     + +++e+ rv+yG+sv+ a+++el+   dvdG L+++a+
  FitnessBrowser__Marino:GFF2201 163 GIVAYEPVWAIGTGKTATPEQVSEVHQQIRQFLAKsapeSADDISEELRVIYGGSVKVANAYELFSLADVDGGLIGGAS 241
                                     **********************************9422234569999******************************** PP

                       TIGR00419 225 lkae 228
                                     l a+
  FitnessBrowser__Marino:GFF2201 242 LHAD 245
                                     *997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (268 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: 21.54
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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 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

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 catabolism of small carbon sources