Alignments for a candidate for tpi in Saccharomonospora cyanea NA-134

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Saccharomonospora cyanea NA-134

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_005455729.1 SACCYDRAFT_RS09590 triose-phosphate isomerase

Query= BRENDA::P9WG43
         (261 letters)



>NCBI__GCF_000244975.1:WP_005455729.1
          Length = 261

 Score =  388 bits (997), Expect = e-113
 Identities = 190/261 (72%), Positives = 215/261 (82%)

Query: 1   MSRKPLIAGNWKMNLNHYEAIALVQKIAFSLPDKYYDRVDVAVIPPFTDLRSVQTLVDGD 60
           M+RKPLIAGNWKMNLNH EAIALVQKIAFSLP+KYY +VDV V+PPFTD+RSVQTLVDGD
Sbjct: 1   MARKPLIAGNWKMNLNHLEAIALVQKIAFSLPEKYYAKVDVTVLPPFTDIRSVQTLVDGD 60

Query: 61  KLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAAT 120
           KL LTYGAQDLSPHDSGAYTGDVSGA LAKLGC+YVVVGHSERR YH E D +V  K   
Sbjct: 61  KLLLTYGAQDLSPHDSGAYTGDVSGAMLAKLGCTYVVVGHSERREYHAETDEVVNKKVRA 120

Query: 121 ALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGTG 180
           ALKHG++PI+C+GE LDVREAGNH+ H   QL  +L GL AEQ+  VV+AYEPVWAIGTG
Sbjct: 121 ALKHGISPILCVGEKLDVREAGNHIEHTTSQLIAALKGLKAEQVEQVVVAYEPVWAIGTG 180

Query: 181 RVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGG 240
           RVA+ ADA+EVCAA+R  L+      +A  +RVLYGGSV + NV D+V  D+VDG LVGG
Sbjct: 181 RVATPADAEEVCAALRSALSDKYGAELAQGIRVLYGGSVKSGNVADLVKCDNVDGALVGG 240

Query: 241 ASLDGEHFATLAAIAAGGPLP 261
           ASLDGE F  L A+AAGGPLP
Sbjct: 241 ASLDGEEFTKLCALAAGGPLP 261


Lambda     K      H
   0.318    0.135    0.393 

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: 294
Number of extensions: 7
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: 261
Length of database: 261
Length adjustment: 25
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_005455729.1 SACCYDRAFT_RS09590 (triose-phosphate 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.28489.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    9.9e-59  184.9   0.5    1.1e-58  184.7   0.5    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005455729.1  SACCYDRAFT_RS09590 triose-phosph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005455729.1  SACCYDRAFT_RS09590 triose-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.7   0.5   1.1e-58   1.1e-58       1     226 [.       6     244 ..       6     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 184.7 bits;  conditional E-value: 1.1e-58
                                 TIGR00419   1 lviinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve.se..iqvaAqnvdav 64 
                                               l+ +n+K+n    +   +v+k+a  + ++  a+v v+v ppf d++ v+  v+  +  ++ +Aq++  +
  lcl|NCBI__GCF_000244975.1:WP_005455729.1   6 LIAGNWKMNLNHLEAIALVQKIAFSLPEKyyAKVDVTVLPPFTDIRSVQTLVDgDKllLTYGAQDLSPH 74 
                                               689***********************9974468899999**********9999544225668******* PP

                                 TIGR00419  65 ksGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaar 133
                                               +sGa+tG++s +ml+ lG+ +v++gHsErR +++e+de+++kkv  + + g+ +++Cvge l+ rea++
  lcl|NCBI__GCF_000244975.1:WP_005455729.1  75 DSGAYTGDVSGAMLAKLGCTYVVVGHSERREYHAETDEVVNKKVRAALKHGISPILCVGEKLDVREAGN 143
                                               ********************************************************************9 PP

                                 TIGR00419 134 tinnvattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvr 194
                                               +i+  + +  aa         e++vvA+EPv++iGtG+++++A+ae+v + +r  l+    +e+a+ +r
  lcl|NCBI__GCF_000244975.1:WP_005455729.1 144 HIEHTTSQLIAALkglkaeqVEQVVVAYEPVWAIGTGRVATPADAEEVCAALRSALSDkYGAELAQGIR 212
                                               999876655554488888999*********************************9987699******** PP

                                 TIGR00419 195 vlyGasvtaaedaelaaqldvdGvLlasavlk 226
                                               vlyG+sv++++ a+l+   +vdG+L+++a+l 
  lcl|NCBI__GCF_000244975.1:WP_005455729.1 213 VLYGGSVKSGNVADLVKCDNVDGALVGGASLD 244
                                               *****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (261 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: 10.75
//
[ok]

This GapMind analysis is from Sep 24 2021. 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 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