Alignments for a candidate for tpi in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for tpi in Desulfobulbus mediterraneus DSM 13871

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_028585663.1 G494_RS0118165 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>NCBI__GCF_000429965.1:WP_028585663.1
          Length = 393

 Score =  375 bits (964), Expect = e-108
 Identities = 193/393 (49%), Positives = 274/393 (69%), Gaps = 6/393 (1%)

Query: 5   TIRDVDLKGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP 63
           T+ ++++ GKRV++RVDFNVP+ + G V DD RI+ ALPTIK  LE+ AKVI+ +H+GRP
Sbjct: 5   TLVELEVSGKRVLVRVDFNVPMTEAGEVADDLRIQTALPTIKLLLERQAKVIICTHMGRP 64

Query: 64  KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGE 123
           KGE  P++SLAPVA+ L+ LL   V   P  +G E +  V  +  GEV++LEN R++  E
Sbjct: 65  KGEKIPKYSLAPVAEYLAALLDLPVTMAPDCIGPEAEAVVAAMAPGEVVMLENLRYYQQE 124

Query: 124 TKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPS-VAGFLMEKEIKFLSKVT 182
             NDP+ A   ASLA+++VNDAF  +HRAHAS VGI + + +  AG L+EKE+ +  +  
Sbjct: 125 VDNDPDFAAQLASLAELYVNDAFAVSHRAHASVVGIPKLMTAKAAGLLLEKELAYFKRSC 184

Query: 183 YNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDK 242
             P++P V ++GGAKVS K+  + N++ + DR+++GGAM  TFLK+ G EVG+S+VEED 
Sbjct: 185 DQPQRPLVAIVGGAKVSGKLEALENMLARVDRLILGGAMANTFLKSQGYEVGASKVEEDL 244

Query: 243 IDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIE 302
           ++ A  LL++A+ + V++ LPVD V A++  P    K V I D IP GWM LDIGP ++ 
Sbjct: 245 LESADRLLQEARRQQVKVYLPVDVVAAERFAPDAVAKQVTIQD-IPPGWMALDIGPASVL 303

Query: 303 LFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNK 362
            F++ L+DAKT+VWNGPMG FE+D F+ GT  +A  +AA     A++V GGGDS AA+  
Sbjct: 304 CFQEVLADAKTIVWNGPMGAFEMDAFSRGTTAIAHCVAA---SHALSVTGGGDSNAAIKL 360

Query: 363 FGLEDKFSHVSTGGGASLEFLEGKELPGIASIA 395
            G     S++STGGGA L  +EGKELPG+A++A
Sbjct: 361 SGEAANISYMSTGGGAFLMLMEGKELPGVAALA 393


Lambda     K      H
   0.317    0.137    0.386 

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: 575
Number of extensions: 35
Number of successful extensions: 5
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: 654
Length of database: 393
Length adjustment: 34
Effective length of query: 620
Effective length of database: 359
Effective search space:   222580
Effective search space used:   222580
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 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