GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Aquimarina longa SW024

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_062061912.1 N456_RS21390 triose-phosphate isomerase

Query= BRENDA::P35144
         (251 letters)



>NCBI__GCF_001401755.1:WP_062061912.1
          Length = 250

 Score =  225 bits (573), Expect = 8e-64
 Identities = 112/249 (44%), Positives = 160/249 (64%)

Query: 1   MRKPIIAGNWKMNKVLSEATSFVEEVKGAVPSPESVDSVVCAPALFLDRLVEATKGTDLK 60
           MRK I+AGNWKMNK L+E  + + E+K  +      + +V   A+ L    E  +  D+K
Sbjct: 1   MRKKIVAGNWKMNKNLAETKTLLSELKTNLQKAREAEVIVAPTAVNLYMATEELQQVDIK 60

Query: 61  IGAQNMHFEENGAFTGEVSPVALADLGVNYVILGHSERREMFAETDETVNQKTIAAFKHG 120
           + AQNMH  ENGA+TGE+S   L  +GV  VILGHSERR  F ETDE +  K   A +H 
Sbjct: 61  VAAQNMHQAENGAYTGEISADMLKRVGVETVILGHSERRAYFGETDELLASKVSKALQHD 120

Query: 121 LTPIVCCGETNEEYEQDQTKTVVANQVQKALAGLTDEQVKQTVIAYEPIWAIGTGKSSTA 180
           +T I C GE  ++ + D    +V NQ++  L  +  E  K  V+AYEP+WAIGTG++++ 
Sbjct: 121 MTVIFCFGEELQDRKSDNHFAIVENQLKNGLFHINTEDWKNVVLAYEPVWAIGTGETASP 180

Query: 181 EGANEVCAYIRSVVAEQFSQDVADAVRIQYGGSVKPANIKEYMSQSDIDGALVGGASLEA 240
           E A E+ A+IR+ +A+ ++Q +AD V I YGGSVKP N  E  ++ D+DG L+GGASL+A
Sbjct: 181 EQAQEMHAFIRNTIAKAYTQQIADEVSILYGGSVKPNNANEIFAKPDVDGGLIGGASLDA 240

Query: 241 DSFLQLLEA 249
           +SF+ ++ A
Sbjct: 241 ESFVAIVNA 249


Lambda     K      H
   0.313    0.129    0.360 

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: 2
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: 251
Length of database: 250
Length adjustment: 24
Effective length of query: 227
Effective length of database: 226
Effective search space:    51302
Effective search space used:    51302
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 (21.9 bits)
S2: 46 (22.3 bits)

Align candidate WP_062061912.1 N456_RS21390 (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.496538.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-70  223.8   1.7    1.4e-70  223.6   1.7    1.0  1  NCBI__GCF_001401755.1:WP_062061912.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001401755.1:WP_062061912.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.6   1.7   1.4e-70   1.4e-70       1     228 []       5     241 ..       5     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 223.6 bits;  conditional E-value: 1.4e-70
                             TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 
                                           +v +n+K+n  + + ++++++l+ ++ +  + ev vap  v l ++++e++  +i+vaAqn++  + Ga+tGe
  NCBI__GCF_001401755.1:WP_062061912.1   5 IVAGNWKMNKNLAETKTLLSELKTNLQKAREAEVIVAPTAVNLYMATEELQqVDIKVAAQNMHQAENGAYTGE 77 
                                           699***********************************************989******************** PP

                             TIGR00419  73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaa 145
                                           isA+mlk +G++ v++gHsErR+++ e+del++ kv+++ + +++++ C ge l++r++ +++  v ++ +  
  NCBI__GCF_001401755.1:WP_062061912.1  78 ISADMLKRVGVETVILGHSERRAYFGETDELLASKVSKALQHDMTVIFCFGEELQDRKSDNHFAIVENQLKNG 150
                                           **********************************************************888888887777665 PP

                             TIGR00419 146 A.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaela 210
                                                   ++++v+A+EPv++iGtG ++s+ +a+++++++r+ ++k  ++++a++v++lyG+sv+ +++ e +
  NCBI__GCF_001401755.1:WP_062061912.1 151 LfhintedWKNVVLAYEPVWAIGTGETASPEQAQEMHAFIRNTIAKaYTQQIADEVSILYGGSVKPNNANEIF 223
                                           55667788**************************************66899********************** PP

                             TIGR00419 211 aqldvdGvLlasavlkae 228
                                           a++dvdG L+++a+l ae
  NCBI__GCF_001401755.1:WP_062061912.1 224 AKPDVDGGLIGGASLDAE 241
                                           ***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (250 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: 15.44
//
[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