GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Rhizorhabdus wittichii RW1

Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_00465
         (263 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  145 bits (367), Expect = 6e-40
 Identities = 90/247 (36%), Positives = 134/247 (54%), Gaps = 21/247 (8%)

Query: 21  KQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIVLDGESIGYD 80
           K Y    VL  V L+++RG+ V L+G+SG+GKTTLL+ +N L E   G I ++G  +   
Sbjct: 9   KHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVA-- 66

Query: 81  DIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPKDEAVALAE 140
                      + +A  R   G  FQ   LFPH++  +NV L + +++ +P++E  A   
Sbjct: 67  ----------AQPVAELRRRIGYVFQGIGLFPHMSVAENVAL-VPRLQGVPREERAARVA 115

Query: 141 KWLERVGL----LERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPELVGE 196
           + L+ V L     ERR   P QLSGGQ QRV  ARA+A  P++ML DE   ALDP    E
Sbjct: 116 ELLDLVALPADFAERR---PAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDE 172

Query: 197 VLNVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSPRLA 255
           +    + L E  G+T L+VTH+M  A  ++D+++ + +GRI    PP+ L      PR+ 
Sbjct: 173 LGAAYRALHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIHGAGDPRIE 232

Query: 256 EFLKNTR 262
             +   R
Sbjct: 233 AMIAVAR 239


Lambda     K      H
   0.320    0.138    0.392 

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: 146
Number of extensions: 6
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: 263
Length of database: 252
Length adjustment: 24
Effective length of query: 239
Effective length of database: 228
Effective search space:    54492
Effective search space used:    54492
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