GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-B in Tatumella morbirosei LMG 23360

Align PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate WP_038021603.1 HA49_RS07395 PTS fructose transporter subunit IIBC

Query= TCDB::D2RXA4
         (150 letters)



>NCBI__GCF_000757425.2:WP_038021603.1
          Length = 570

 Score = 82.0 bits (201), Expect = 1e-20
 Identities = 51/131 (38%), Positives = 74/131 (56%), Gaps = 6/131 (4%)

Query: 2   KFVAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVII 61
           + VAVT+CPTG+AH+ MAAE +E  A  RG    VE +G++G  N ++ + +A AD VI+
Sbjct: 115 RIVAVTACPTGVAHTFMAAEAIEAEAKKRGWWYKVETRGSVGAGNAITPEEVAAADLVIV 174

Query: 62  AADTSVNQDRFEGKPVVTAPVKDAVNDVEDLLERAIAAADGETSTADSAQSEGAADASAS 121
           AAD  V+  +F GKP+       A+       ++A++ A    S A + QS     AS S
Sbjct: 175 AADIEVDLAKFAGKPMYRTSTSLALKKTAQEFDKALSEAK-TFSPAGNNQS-----ASNS 228

Query: 122 DAEAADSGAPR 132
           D+    SGA R
Sbjct: 229 DSNKEKSGAYR 239



 Score = 41.6 bits (96), Expect = 2e-08
 Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 55  EADAVIIAADTSVNQDRFEGKPVVTAPVKDAVNDVEDLLERAIAAADGETSTADSAQSEG 114
           EA+ VI+A  T  + +   GK +    ++  +ND E  L +A   A  E   A  A +  
Sbjct: 40  EAELVIVAGGTVPSDNTLSGKKIWQGGLQALLNDAEAFLHQAKEQA--ELWQAPQAMNAA 97

Query: 115 AADASASDAEAADSGAPR 132
           AADA+A+DA A+++ A R
Sbjct: 98  AADAAAADAAASNTTAKR 115


Lambda     K      H
   0.307    0.122    0.323 

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: 128
Number of extensions: 5
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 150
Length of database: 570
Length adjustment: 26
Effective length of query: 124
Effective length of database: 544
Effective search space:    67456
Effective search space used:    67456
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 47 (22.7 bits)

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