GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Geotalea uraniireducens Rf4

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>NCBI__GCF_000016745.1:WP_011938227.1
          Length = 353

 Score =  152 bits (384), Expect = 9e-42
 Identities = 92/246 (37%), Positives = 143/246 (58%), Gaps = 10/246 (4%)

Query: 16  LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75
           L + DLH   G   +LKGV L + +G +V L+G SGSGKTTLLR +  LE    G I + 
Sbjct: 6   LSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRI- 64

Query: 76  GESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHKD 135
           GE + +   + K++      ++  +   G  FQ + L+PH T  +NV  GL K++K+   
Sbjct: 65  GEQMVFE--SAKKIE-----VSVEKRCLGFVFQSYALWPHRTVYENVAYGL-KLRKVPDG 116

Query: 136 EAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPEL 195
           E     ++ L  +GL +  + +P QLSGGQQQRVA+AR++  NP ++L DE  S LD +L
Sbjct: 117 EIRQRVQEVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKL 176

Query: 196 VGEVLSVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQSP 254
             E    ++ L  D  ++ + VTH+   A  ++DK+V +  G IE+ G P+E++  P+S 
Sbjct: 177 REEARIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSL 236

Query: 255 RLAEFL 260
            +AEF+
Sbjct: 237 FVAEFM 242


Lambda     K      H
   0.319    0.135    0.379 

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: 209
Number of extensions: 8
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: 265
Length of database: 353
Length adjustment: 27
Effective length of query: 238
Effective length of database: 326
Effective search space:    77588
Effective search space used:    77588
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: 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