Alignments for a candidate for tpi in Arenitalea lutea P7-3-5

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Arenitalea lutea P7-3-5

Align triosephosphate isomerase subunit (EC 5.3.1.1) (characterized)
to candidate WP_019388787.1 P735_RS0114590 triose-phosphate isomerase

Query= metacyc::MONOMER-13051
         (252 letters)



>NCBI__GCF_000283015.1:WP_019388787.1
          Length = 249

 Score =  223 bits (568), Expect = 3e-63
 Identities = 114/247 (46%), Positives = 162/247 (65%), Gaps = 1/247 (0%)

Query: 3   RTPIIAGNWKLNMNPKETVEFVNAVKDQLPDPSKVESVICAPAVDLDALLKAAEGSNLHV 62
           R  I+AGNWK+N +  +T   + A+K Q    +  E +I   A +L     + + S + V
Sbjct: 2   RKQIVAGNWKMNNDLAQTEALITALKKQTKT-TDAEVMIAPTATNLWQAYNSLKDSKIEV 60

Query: 63  GAENCYWENSGAFTGETSPAVLKEMGVQYVIIGHSERRDYFHETDEDINKKAKAIFANGL 122
            A+N ++  +GA+TGE S ++LK +G+  VI+GHSERR+YF+ETDE + KK  A  A G+
Sbjct: 61  IAQNMHFAENGAYTGEISASMLKSIGINTVILGHSERREYFNETDELLAKKVDAALAKGM 120

Query: 123 TPILCCGESLETREAGKENEWVVSQIKAGLEGLTSEQVSKLVIAYEPIWAIGTGKTASSD 182
             I C GE L  R+AGKE   V +QIK  L  L +     +++AYEP+WAIGTG+TAS +
Sbjct: 121 RVIFCFGEELADRKAGKEETVVGNQIKNALFHLNAAAFQNIILAYEPVWAIGTGETASPE 180

Query: 183 QAEEMCKTIRETVKDLYNEETAENVRIQYGGSVKPANVKELMAKPNIDGGLVGGASLVPD 242
           QA++M   IR+T+ D Y  + AE V I YGGSVKPAN +E+ +KP++DGGL+GGASL  D
Sbjct: 181 QAQDMHAFIRKTLADKYGNDIAEEVSILYGGSVKPANAEEIFSKPDVDGGLIGGASLNAD 240

Query: 243 SYLALVN 249
            + A+VN
Sbjct: 241 DFFAIVN 247


Lambda     K      H
   0.312    0.130    0.377 

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: 178
Number of extensions: 7
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: 252
Length of database: 249
Length adjustment: 24
Effective length of query: 228
Effective length of database: 225
Effective search space:    51300
Effective search space used:    51300
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 46 (22.3 bits)

Align candidate WP_019388787.1 P735_RS0114590 (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.1300262.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.2e-68  216.5   1.1    2.5e-68  216.3   1.1    1.0  1  NCBI__GCF_000283015.1:WP_019388787.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000283015.1:WP_019388787.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.3   1.1   2.5e-68   2.5e-68       1     228 []       5     240 ..       5     240 .. 0.97

  Alignments for each domain:
  == domain 1  score: 216.3 bits;  conditional E-value: 2.5e-68
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           +v +n+K+n+ + + e +++ l+++  ++++ ev +ap    l  + + ++ s+i+v Aqn++  + Ga+tGe
  NCBI__GCF_000283015.1:WP_019388787.1   5 IVAGNWKMNNDLAQTEALITALKKQT-KTTDAEVMIAPTATNLWQAYNSLKdSKIEVIAQNMHFAENGAYTGE 76 
                                           699*******************9985.78899******************99********************* PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138
                                           isA mlk +G++ v++gHsErR +++e+del++kkv  + ++g++++ C ge l++r+       ++++i+n 
  NCBI__GCF_000283015.1:WP_019388787.1  77 ISASMLKSIGINTVILGHSERREYFNETDELLAKKVDAALAKGMRVIFCFGEELADRKagkeetvVGNQIKNA 149
                                           ********************************************************99888888888999999 PP

                             TIGR00419 139 attaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaela 210
                                           +   +aaA+++ ++A+EPv++iGtG ++s+ +a+ +++++r  l+    +++ae+v++lyG+sv+ a++ e +
  NCBI__GCF_000283015.1:WP_019388787.1 150 LFHLNAAAFQNIILAYEPVWAIGTGETASPEQAQDMHAFIRKTLADkYGNDIAEEVSILYGGSVKPANAEEIF 222
                                           99999************************************999977999*********************** PP

                             TIGR00419 211 aqldvdGvLlasavlkae 228
                                            ++dvdG L+++a+l a+
  NCBI__GCF_000283015.1:WP_019388787.1 223 SKPDVDGGLIGGASLNAD 240
                                           ***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (249 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: 23.68
//
[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 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