GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1747 in Rhodobacter johrii JA192

Align TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_002722145.1 C8J29_RS19495 ABC transporter permease subunit

Query= TCDB::Q9X269
         (341 letters)



>NCBI__GCF_003046325.1:WP_002722145.1
          Length = 307

 Score =  230 bits (586), Expect = 4e-65
 Identities = 119/319 (37%), Positives = 189/319 (59%), Gaps = 15/319 (4%)

Query: 25  LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84
           L++ L+RL +   ++ +++ +T+ ++ LAPG  F+L+R          P DP     LK 
Sbjct: 2   LRYTLRRLASAVPTVFIIVTLTFFMIRLAPGGPFDLER----------PLDPLIMENLK- 50

Query: 85  FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144
               Y L+  LW Q L Y+   +    GPSF+     + DL     PI+  L   +I  A
Sbjct: 51  --RAYNLDGSLWSQYLTYMGNLMQGDLGPSFTKRDFTVNDLFASGLPISMLLGGLAISLA 108

Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWEG 204
           +++G  LG +AAL++N+W+DYT + ++  G+  P++VVA  L L F + L WLP  GW  
Sbjct: 109 VLIGTILGAIAALRQNSWLDYTIVGLATFGITTPNFVVAPLLSLFFGVILRWLPAGGWSS 168

Query: 205 IRTK--ILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPS 262
                 +LP + LAL  +A +AR  R + ++ L  + +RTA A G   RTV++KHALR +
Sbjct: 169 SDPAYWVLPVVTLALPQVAVIARLVRGATIEALRSNHVRTARAYGLPARTVVVKHALRAA 228

Query: 263 MIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMI 322
           M+P V+ +GP  A L+ G+V VE IF +PG+G+ F   A+ RDY L++ +  ++AL +++
Sbjct: 229 MLPAVSYLGPTAAGLLTGSVVVETIFGLPGIGRYFVQGALGRDYTLVMGTVVVIALFILL 288

Query: 323 MNLIVDVLYAILDPRIKLD 341
            NLIVD+LY +LDPR++ D
Sbjct: 289 FNLIVDLLYTLLDPRVRYD 307


Lambda     K      H
   0.328    0.143    0.429 

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: 326
Number of extensions: 21
Number of successful extensions: 3
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: 341
Length of database: 307
Length adjustment: 28
Effective length of query: 313
Effective length of database: 279
Effective search space:    87327
Effective search space used:    87327
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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