GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Collimonas arenae Ter10

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_082797906.1 CAter10_RS13300 triose-phosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>NCBI__GCF_001584165.1:WP_082797906.1
          Length = 248

 Score =  234 bits (598), Expect = 1e-66
 Identities = 123/249 (49%), Positives = 160/249 (64%), Gaps = 1/249 (0%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60
           MR  LV GNWK+NGS      L++ ++   A  A C VA+  P  Y+   +    GS I 
Sbjct: 1   MRRKLVAGNWKMNGSLVANAALLAEIKAGAAAPA-CDVALCVPAPYLAQCQAALAGSAIA 59

Query: 61  LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120
            G Q+V  + +GA+TGE S +ML+D   +Y+I+GHSERR YH ESD ++A+K     E G
Sbjct: 60  WGGQDVSAHTAGAYTGEVSVSMLEDFSCRYVIVGHSERRAYHAESDAVVAQKVLRALEAG 119

Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180
           +TP++C+GET AE EAG+TE V  RQ+DAVL     A     V+AYEPVWAIGTGK+ATP
Sbjct: 120 VTPIVCVGETLAEREAGQTEAVVGRQLDAVLNVLADADLARIVVAYEPVWAIGTGKTATP 179

Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240
             AQ VH  +R  +AK +A  A +V I YGGS+   NA EL A PDIDG L+GGA+LK+ 
Sbjct: 180 QMAQDVHLALRAQLAKKNAAAALEVKILYGGSMKPDNAVELLAMPDIDGGLIGGAALKSA 239

Query: 241 AFAVIVKAA 249
            F  I+ AA
Sbjct: 240 DFLAIIAAA 248


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: 185
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: 255
Length of database: 248
Length adjustment: 24
Effective length of query: 231
Effective length of database: 224
Effective search space:    51744
Effective search space used:    51744
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: 46 (22.3 bits)

Align candidate WP_082797906.1 CAter10_RS13300 (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.1278832.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.4e-64  202.8   4.8      4e-64  202.5   4.8    1.0  1  NCBI__GCF_001584165.1:WP_082797906.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001584165.1:WP_082797906.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.5   4.8     4e-64     4e-64       1     227 [.       5     238 ..       5     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 202.5 bits;  conditional E-value: 4e-64
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           lv +n+K+n+s+   + ++a++++  a +  + va+ +p  +l   + ++  s i  + q+v a+++Ga+tGe
  NCBI__GCF_001584165.1:WP_082797906.1   5 LVAGNWKMNGSLVANAALLAEIKAGAAAP-ACDVALCVPAPYLAQCQAALAgSAIAWGGQDVSAHTAGAYTGE 76 
                                           799********************976655.47788888888899999999889******************** PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138
                                           +s  ml+d+ +++v++gHsErR++++e+d ++++kv r+ e g++++vCvgetl+ere       ++r++++v
  NCBI__GCF_001584165.1:WP_082797906.1  77 VSVSMLEDFSCRYVIVGHSERRAYHAESDAVVAQKVLRALEAGVTPIVCVGETLAEREagqteavVGRQLDAV 149
                                           **********************************************************999999889999999 PP

                             TIGR00419 139 attaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211
                                           ++  a a l   vvA+EPv++iGtGk++++  a+ v+  +r  l+k ++  a +v++lyG+s++  +++el a
  NCBI__GCF_001584165.1:WP_082797906.1 150 LNVLADADLARIVVAYEPVWAIGTGKTATPQMAQDVHLALRAQLAKKNAAAALEVKILYGGSMKPDNAVELLA 222
                                           99999999***************************************************************** PP

                             TIGR00419 212 qldvdGvLlasavlka 227
                                            +d+dG L+++a lk+
  NCBI__GCF_001584165.1:WP_082797906.1 223 MPDIDGGLIGGAALKS 238
                                           *************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (248 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: 13.47
//
[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