GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Arenitalea lutea P7-3-5

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_019388681.1 P735_RS0114015 ATP-binding cassette domain-containing protein

Query= TCDB::Q9X272
         (328 letters)



>NCBI__GCF_000283015.1:WP_019388681.1
          Length = 227

 Score =  105 bits (262), Expect = 1e-27
 Identities = 70/213 (32%), Positives = 118/213 (55%), Gaps = 16/213 (7%)

Query: 12  PLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG 71
           P+LQ  D   +  QG  ++  +  +++EI +GE + L+G++G GKS+  +T+   L    
Sbjct: 4   PILQLKDASIF--QGDSLV--LSNVNVEINKGEFVYLIGKTGTGKSSFMKTLYGDLPLTE 59

Query: 72  GKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGT--- 128
           G+      D+ NL +K++   R+K+ ++FQD       ++   R I D L+     T   
Sbjct: 60  GEGHIVDFDLKNLKEKDIPYLRRKLGVVFQDF------KLLTDRTINDNLLFVLKATGWK 113

Query: 129 -KKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSAL 187
            K + + RVEE+L  V +  +    FPHE SGG+QQR+ IARAL  NP+ I+ DEP   L
Sbjct: 114 DKDKMKTRVEEVLTKVDMKTKGFK-FPHELSGGEQQRVAIARALLNNPELILADEPTGNL 172

Query: 188 DVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVV 220
           D     +++++L++I  K G + L   H+ A++
Sbjct: 173 DPQTSVEVMEVLQDI-NKNGNTILMATHDYALL 204


Lambda     K      H
   0.321    0.142    0.417 

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: 194
Number of extensions: 12
Number of successful extensions: 2
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: 328
Length of database: 227
Length adjustment: 25
Effective length of query: 303
Effective length of database: 202
Effective search space:    61206
Effective search space used:    61206
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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