GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Acidovorax sp. GW101-3H11

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Ac3H11_4404 Phosphoglycerate kinase (EC 2.7.2.3)

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4404
          Length = 399

 Score =  313 bits (803), Expect = 7e-90
 Identities = 177/381 (46%), Positives = 244/381 (64%), Gaps = 13/381 (3%)

Query: 12  KGKRVIMRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP-KGEPSP 69
           +G+RV +R D NVP  D G + +DTRIRA++P I+ AL+ GA V++ SHLGRP +GE  P
Sbjct: 16  QGQRVFIRADMNVPQDDAGQITEDTRIRASIPCIRMALDAGAAVMVTSHLGRPTEGEFKP 75

Query: 70  EFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPE 129
           E SLAPVA+RLSELLG++V  V   V D V  A      G+V+LLEN R + GE KN  E
Sbjct: 76  EDSLAPVAQRLSELLGRDVPLVANWV-DGVTVA-----PGQVVLLENCRLNVGEKKNKDE 129

Query: 130 LAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVTYNPEKP 188
           LA+  A+L DI VNDAFGTAHRA  +  GIAQF P + AG L+  EI  L+K    P++P
Sbjct: 130 LARKLAALCDIFVNDAFGTAHRAEGTTYGIAQFAPVACAGPLLSAEIDALTKALAQPQRP 189

Query: 189 YVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKE 248
              ++ G+KVS K+ ++ +L +K D++++GG +  TF+ A G  +G S  E D +D AK 
Sbjct: 190 LAAIVAGSKVSTKLTILQSLADKVDQLIVGGGIANTFMLAAGLPIGKSLAEPDLLDAAKS 249

Query: 249 LLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKL 308
           ++   K +G E+ +P D V+A+         V    D  P+  + LDIGP+T      +L
Sbjct: 250 VMAAMKARGAEVPIPTDVVVAKAFAADAPATVKAATDVAPDDLI-LDIGPDTAARLAAQL 308

Query: 309 SDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGLEDK 368
             A T+VWNGP+GVFE   F  GT+ +A AIA   E  A ++ GGGD+ AA+ K+G+E +
Sbjct: 309 KSAGTIVWNGPVGVFEFAAFENGTRALAAAIA---ESPAFSIAGGGDTLAAIAKYGIEKQ 365

Query: 369 FSHVSTGGGASLEFLEGKELP 389
             ++STGGGA LE LEGK+LP
Sbjct: 366 VGYISTGGGAFLEVLEGKKLP 386


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: 561
Number of extensions: 23
Number of successful extensions: 7
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: 399
Length adjustment: 34
Effective length of query: 620
Effective length of database: 365
Effective search space:   226300
Effective search space used:   226300
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 17 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