GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Snodgrassella alvi wkB2

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_025331459.1 SALWKB2_RS09585 triose-phosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>NCBI__GCF_000600005.1:WP_025331459.1
          Length = 251

 Score =  192 bits (489), Expect = 4e-54
 Identities = 108/248 (43%), Positives = 153/248 (61%), Gaps = 7/248 (2%)

Query: 6   VMGNWKLNGSRHMVHELVSNLRKEL-AGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQ 64
           V+GNWK+NGS      L+  L + + A  A     IA P +Y+   K  A  + + +GA+
Sbjct: 7   VIGNWKMNGSNAANRTLLQELLQPVNAAAAQVYCGIAAPNVYLAGIKEFAANTALAVGAE 66

Query: 65  NVD-LNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTP 123
           +V    ++GAFTGE SA ML D+GAQ++++GHSERR Y +E + ++ +K       GL P
Sbjct: 67  DVSRFAVNGAFTGEVSAQMLADVGAQFVLVGHSERRQYFQEDNTILLEKMQNSIAAGLLP 126

Query: 124 VLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQA 183
           +LC+GET AE +AG+ E+V A Q+  + +    A      +AYEPVWAIGTGK     Q 
Sbjct: 127 ILCVGETLAERDAGQEEQVVAAQLSLLAE----ADLSEVAVAYEPVWAIGTGKVPVTEQI 182

Query: 184 QAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFA 243
            A+H+ I   I  +      ++ + YGGSVNA NAAE+ A   +DGALVGGASL+AD+FA
Sbjct: 183 AAMHELIYRQILSLCGKDV-KIRVLYGGSVNAGNAAEILAVSHVDGALVGGASLQADSFA 241

Query: 244 VIVKAAEA 251
            I++AA A
Sbjct: 242 AIIQAAYA 249


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: 179
Number of extensions: 6
Number of successful extensions: 4
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: 251
Length adjustment: 24
Effective length of query: 231
Effective length of database: 227
Effective search space:    52437
Effective search space used:    52437
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_025331459.1 SALWKB2_RS09585 (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.1272807.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.4e-57  179.0   4.2    7.3e-57  178.8   4.2    1.0  1  NCBI__GCF_000600005.1:WP_025331459.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000600005.1:WP_025331459.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.8   4.2   7.3e-57   7.3e-57       2     228 .]       7     238 ..       6     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 7.3e-57
                             TIGR00419   2 viinfKlnesvgkvelevaklaeev.aseagvevavappfvdldvvkdeve.seiqvaAqnvda.vksGaftG 71 
                                           vi+n+K+n+s     +++++l + v a  a+v+ ++a p v+l  +k+ +  + + v+A +v      GaftG
  NCBI__GCF_000600005.1:WP_025331459.1   7 VIGNWKMNGSNAANRTLLQELLQPVnAAAAQVYCGIAAPNVYLAGIKEFAAnTALAVGAEDVSRfAVNGAFTG 79 
                                           89********************977477899****************9766599********862568***** PP

                             TIGR00419  72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa 144
                                           e+sA+ml+d+Ga++vl+gHsErR +++e + ++ +k+ +  + gl +++Cvgetl+er+a+++ ++va + + 
  NCBI__GCF_000600005.1:WP_025331459.1  80 EVSAQMLADVGAQFVLVGHSERRQYFQEDNTILLEKMQNSIAAGLLPILCVGETLAERDAGQEEQVVAAQLSL 152
                                           **********************************************************************998 PP

                             TIGR00419 145 aA...lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaelaaql 213
                                            A   l+++ vA+EPv++iGtGk+    +  ++++ +   +     k+v  ++rvlyG+sv+a+++ae  a  
  NCBI__GCF_000600005.1:WP_025331459.1 153 LAeadLSEVAVAYEPVWAIGTGKVPVTEQIAAMHELIYRQILSlCGKDV--KIRVLYGGSVNAGNAAEILAVS 223
                                           88889******************99999999999999766655478887..589******************* PP

                             TIGR00419 214 dvdGvLlasavlkae 228
                                            vdG+L+++a+l+a+
  NCBI__GCF_000600005.1:WP_025331459.1 224 HVDGALVGGASLQAD 238
                                           ************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (251 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: 16.32
//
[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