GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Collinsella tanakaei YIT 12063

Align triosephosphate isomerase subunit (EC 5.3.1.1) (characterized)
to candidate WP_009140074.1 HMPREF9452_RS00185 triose-phosphate isomerase

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



>NCBI__GCF_000225705.1:WP_009140074.1
          Length = 257

 Score =  266 bits (681), Expect = 2e-76
 Identities = 130/248 (52%), Positives = 170/248 (68%), Gaps = 1/248 (0%)

Query: 2   SRTPIIAGNWKLNMNPKETVEFVNAVKDQLPDPSK-VESVICAPAVDLDALLKAAEGSNL 60
           +RT +IAGNWK+N + +      + +   L      VE ++C P +DL  +    +GS +
Sbjct: 5   NRTLLIAGNWKMNNDVQAAATLADELVAALDGVDNGVEVLVCPPTIDLTTVAAKLDGSAI 64

Query: 61  HVGAENCYWENSGAFTGETSPAVLKEMGVQYVIIGHSERRDYFHETDEDINKKAKAIFAN 120
            +GA+N YWE +GA+TGE+S  +LK  G  Y IIGHSERRDYFHETDED NKKAKA+ A 
Sbjct: 65  KLGAQNVYWEAAGAYTGESSCDMLKSAGCTYCIIGHSERRDYFHETDEDQNKKAKALVAA 124

Query: 121 GLTPILCCGESLETREAGKENEWVVSQIKAGLEGLTSEQVSKLVIAYEPIWAIGTGKTAS 180
           GL P+ CCGE LE REAG   E VV+Q+KAGLEGL     ++LV+AYEPIWAIGTG TA+
Sbjct: 125 GLVPVFCCGEPLEVREAGTYVEHVVAQVKAGLEGLEIADPAQLVVAYEPIWAIGTGMTAT 184

Query: 181 SDQAEEMCKTIRETVKDLYNEETAENVRIQYGGSVKPANVKELMAKPNIDGGLVGGASLV 240
           +D A+E+C  +RE + DL+  E A  +R+ YGGS KP N+ EL AKP++DG LVGGASL 
Sbjct: 185 ADDAQEVCAAVREALADLFGAELASGIRVLYGGSAKPGNIAELTAKPDVDGALVGGASLK 244

Query: 241 PDSYLALV 248
              +  +V
Sbjct: 245 AADFSQMV 252


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: 174
Number of extensions: 8
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: 257
Length adjustment: 24
Effective length of query: 228
Effective length of database: 233
Effective search space:    53124
Effective search space used:    53124
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: 47 (22.7 bits)

Align candidate WP_009140074.1 HMPREF9452_RS00185 (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.2990586.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.3e-60  191.1   1.6    1.5e-60  190.8   1.6    1.0  1  NCBI__GCF_000225705.1:WP_009140074.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000225705.1:WP_009140074.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   1.6   1.5e-60   1.5e-60       1     227 [.       9     245 ..       9     246 .. 0.95

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 1.5e-60
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevasea.gvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftG 71 
                                           l+ +n+K+n+ v+  +++  +l + + +++ gvev v pp +dl +v+ +++ s i+++Aqnv    +Ga+tG
  NCBI__GCF_000225705.1:WP_009140074.1   9 LIAGNWKMNNDVQAAATLADELVAALDGVDnGVEVLVCPPTIDLTTVAAKLDgSAIKLGAQNVYWEAAGAYTG 81 
                                           689*********************99987538********************9******************** PP

                             TIGR00419  72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa 144
                                           e s +mlk +G+ + +igHsErR +++e+de  +kk   l + gl +v C ge le rea++ ++ v  + +a
  NCBI__GCF_000225705.1:WP_009140074.1  82 ESSCDMLKSAGCTYCIIGHSERRDYFHETDEDQNKKAKALVAAGLVPVFCCGEPLEVREAGTYVEHVVAQVKA 154
                                           *******************************************************************999998 PP

                             TIGR00419 145 aA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedael 209
                                                      + vvA+EP+++iGtG++++  +a++v + vr+ l+    +e+a  +rvlyG+s + ++ ael
  NCBI__GCF_000225705.1:WP_009140074.1 155 GLegleiadPAQLVVAYEPIWAIGTGMTATADDAQEVCAAVREALADlFGAELASGIRVLYGGSAKPGNIAEL 227
                                           66676664556779********************************9899*********************** PP

                             TIGR00419 210 aaqldvdGvLlasavlka 227
                                            a++dvdG+L+++a+lka
  NCBI__GCF_000225705.1:WP_009140074.1 228 TAKPDVDGALVGGASLKA 245
                                           *****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 13.19
//
[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:

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:

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:

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:

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