GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Pseudarthrobacter sulfonivorans Ar51

Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_058929075.1 AU252_RS00670 branched-chain amino acid ABC transporter permease

Query= ecocyc::LIVH-MONOMER
         (308 letters)



>NCBI__GCF_001484605.1:WP_058929075.1
          Length = 291

 Score =  137 bits (344), Expect = 4e-37
 Identities = 88/291 (30%), Positives = 148/291 (50%), Gaps = 9/291 (3%)

Query: 12  MFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDTGWL 71
           +F G+ LG+ Y L+A G +++YG++G++NFAHG    +G++  + I       G D  W 
Sbjct: 8   LFTGLGLGALYFLVAAGLSLIYGLMGVLNFAHGAFLTLGAFTGWEIARRT---GSDNWWT 64

Query: 72  LVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEGSRDV 131
            + +  VGA+   + +    E V  R +   + +  ++  +G+S+     V+L +G    
Sbjct: 65  FLLSLLVGAVA-GAVFAAFTEFVLIRRLYQ-RHIEQVLITVGLSLAA---VALFDGIWGT 119

Query: 132 ALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRACAEDL 191
               +    W    +E   A I   + +  I   L +LAL  F++ +R G   RA  E+ 
Sbjct: 120 DPVFIQGPAWFKETTEILGARIPNDRFICIIAAVLVLLALVFFLKNTRYGMIIRAGVENR 179

Query: 192 KMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAAVLGGI 251
            M + LGI+  +   L F IG A A + GVL   ++G ++P +G    + AF   V+GG+
Sbjct: 180 SMVTALGIDVRKAFTLVFTIGGAAAGLGGVLASHYFGYVSPLLGGSLLIFAFIVTVIGGL 239

Query: 252 GSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGR 302
           GS+ GA I  + + + +  ++ YL      VV  A L LVLL  P+G+LGR
Sbjct: 240 GSLTGAAIAAVAVAVLQQFANFYLGGTGDFVVVLA-LALVLLFRPSGLLGR 289


Lambda     K      H
   0.328    0.141    0.410 

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: 225
Number of extensions: 12
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: 308
Length of database: 291
Length adjustment: 27
Effective length of query: 281
Effective length of database: 264
Effective search space:    74184
Effective search space used:    74184
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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