GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Rhizorhabdus wittichii RW1

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  108 bits (271), Expect = 8e-29
 Identities = 79/236 (33%), Positives = 120/236 (50%), Gaps = 20/236 (8%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           ++    V K + G   L+ V +TIERG    L+G +GAGKTT    I  L + DTGT  +
Sbjct: 1   MISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAI 60

Query: 65  DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124
           +G+  +     E+ +  I   FQ I LF  M+V ENV +   V   Q V          R
Sbjct: 61  EGRDVAAQPVAELRRR-IGYVFQGIGLFPHMSVAENVAL---VPRLQGV---------PR 107

Query: 125 EEEAAIREKSQKLLDFVGI-GQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183
           EE AA   +  +LLD V +   FA+R    LS G  +R+  ARALA  P ++ +DEP   
Sbjct: 108 EERAA---RVAELLDLVALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGA 164

Query: 184 MN--ATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVP 237
           ++    ++LG     +  +A G T L++ HD+   + L +R+ V+  G+ +A+  P
Sbjct: 165 LDPVTRDELGAAYRALH-EAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPP 219


Lambda     K      H
   0.320    0.138    0.394 

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: 160
Number of extensions: 7
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: 255
Length of database: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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 Apr 09 2024. 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