GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Rhodococcus qingshengii djl-6-2

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_007728726.1 C1M55_RS16600 branched-chain amino acid ABC transporter permease

Query= TCDB::Q8DQI0
         (292 letters)



>NCBI__GCF_002893965.1:WP_007728726.1
          Length = 448

 Score =  157 bits (397), Expect = 4e-43
 Identities = 97/286 (33%), Positives = 157/286 (54%), Gaps = 4/286 (1%)

Query: 4   MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFV 63
           +++  V+GL  G V A+  +G +++YG   L NFAHG++  +GA   + +  SF +    
Sbjct: 157 LIRTTVDGLRFGLVIAIAGVGLSLIYGTTGLTNFAHGEMVTLGAVAAWVINTSFGVPLIP 216

Query: 64  ALIVAMLATAILGVVIEFLAYRPLRHSTR--IAVLITAIGVSFLLEYGMVYLVGANTRAF 121
           A I+A+     +G++   + ++PLR      IA L+ +IG++  L Y ++         F
Sbjct: 217 ATILAIFVGIGIGLLTNGIVWKPLRKRKTGLIAQLVVSIGLAISLRYLILIFFSDRAEPF 276

Query: 122 PQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLM 181
                 V  + GPI+LT+   +++ +SL++++ + +++QKT++GKAMRAVS + D A   
Sbjct: 277 DDYQGQVEKNWGPIALTDANAIVMIVSLVVLVGVALLLQKTRIGKAMRAVSDNRDLAASS 336

Query: 182 GINVNRTISFTFALGSALAGAAGVL--IALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIP 239
           GINV R I F + LG  LA   GVL  I+     ++  MG    L  F    LGG+G   
Sbjct: 337 GINVERVIMFVWGLGGGLAALGGVLFGISELGGRVQWEMGFKLLLLMFAGITLGGLGTAY 396

Query: 240 GAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILG 285
           GA LG  ++GLL   +T     D +      +L++IL+VRP GILG
Sbjct: 397 GALLGCVIVGLLVQLSTLIINPDLKYIGGLLVLIVILVVRPQGILG 442


Lambda     K      H
   0.330    0.146    0.407 

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: 255
Number of extensions: 10
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: 292
Length of database: 448
Length adjustment: 29
Effective length of query: 263
Effective length of database: 419
Effective search space:   110197
Effective search space used:   110197
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 (21.8 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