GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Stutzerimonas stutzeri A1501

Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

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



>NCBI__GCF_000013785.1:WP_011911265.1
          Length = 279

 Score =  241 bits (616), Expect = 9e-69
 Identities = 134/250 (53%), Positives = 168/250 (67%), Gaps = 2/250 (0%)

Query: 11  QPLLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQI 70
           QP++    + K+YG L VL+G+DL +Q G  V +IG SGSGK+TLLR +  LE    G I
Sbjct: 23  QPMVRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTLEGIDDGLI 82

Query: 71  VLDGESIGY-DDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKK 129
            +DGE + +  D  G+ V    + + R R   GM FQ FNLFPH+ ALQNV    ++V  
Sbjct: 83  EVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQVLG 142

Query: 130 LPKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSAL 189
           L K EA   AE+ L  VGL ++ +HFP QLSGGQQQRVAIARA+AM P +MLFDEVTSAL
Sbjct: 143 LSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVTSAL 202

Query: 190 DPELVGEVLNVIKGLAE-DGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFER 248
           DPEL GEVL+VI+ L E   +TML+VTH+M FA E +D++ F +QGRI EQG P  LF  
Sbjct: 203 DPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDALFNN 262

Query: 249 PQSPRLAEFL 258
           PQ  R  EFL
Sbjct: 263 PQEDRTREFL 272


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: 213
Number of extensions: 9
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: 263
Length of database: 279
Length adjustment: 25
Effective length of query: 238
Effective length of database: 254
Effective search space:    60452
Effective search space used:    60452
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