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_084295488.1 C8J29_RS21175 ABC transporter permease

Query= TCDB::Q9X269
         (341 letters)



>NCBI__GCF_003046325.1:WP_084295488.1
          Length = 317

 Score =  206 bits (524), Expect = 6e-58
 Identities = 108/328 (32%), Positives = 193/328 (58%), Gaps = 20/328 (6%)

Query: 22  MRFLKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQAT 81
           M  L+FL++R+++    + VV ++T+ L+ + PG         D  A +   +  A Q  
Sbjct: 1   MTVLRFLIRRMVSAVPVLFVVSLVTFALIAIVPG---------DVTAELAGAEATAEQRA 51

Query: 82  LKGFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSI 141
           +    ++ GLN PL++Q L +    +    G S+     ++ D + E+ P+T +LA  ++
Sbjct: 52  V--LRDQLGLNQPLYQQALRWYGNLLQGDLGHSYL-LNMSVTDAVLERLPVTLSLAGLAL 108

Query: 142 LFALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSG 201
           + A+V+GV LG+LAA++ ++W+D   M+V++IG+++P + + + +I +FS+ L W PT G
Sbjct: 109 VLAVVLGVLLGVLAAIRHDSWVDQGTMSVALIGLSVPDFWLGLIMISVFSVGLAWFPTGG 168

Query: 202 WEGI--------RTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTV 253
           +           R+  LP +ALA   +  +AR TR S+L+ + QD+IRTA AKG    TV
Sbjct: 169 YVPFSEDALGWARSMALPALALAFTQMGVIARMTRSSMLEVMGQDYIRTARAKGMRRHTV 228

Query: 254 IMKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTST 313
           + KHALR +++P++T++G     L+ G V +E++F +PG+G+L   A   RD+P++    
Sbjct: 229 VFKHALRNALVPVITVIGVMTGVLLGGAVVIESVFSLPGVGRLIIGAIQRRDFPIIQGGL 288

Query: 314 FILALTVMIMNLIVDVLYAILDPRIKLD 341
            I A   + +N++VD+ Y   DPR++ D
Sbjct: 289 LITASLFVFVNILVDLAYGWFDPRVRND 316


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: 307
Number of extensions: 12
Number of successful extensions: 4
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: 317
Length adjustment: 28
Effective length of query: 313
Effective length of database: 289
Effective search space:    90457
Effective search space used:    90457
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: 49 (23.5 bits)

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

Links

Downloads

Related tools

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