GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Thiothrix lacustris DSM 21227

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

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



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  148 bits (374), Expect = 1e-40
 Identities = 93/247 (37%), Positives = 141/247 (57%), Gaps = 16/247 (6%)

Query: 15  LLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILL 74
           +L + ++ K++   EVL   +LT+Q G   T++G SG GKTT+LR +   E+   GQILL
Sbjct: 6   ILTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILL 65

Query: 75  DGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHK 134
           +G+ I              ++ A+ R      FQ + LFPHLT   NV  GL       +
Sbjct: 66  NGDDIA-------------RIPAEKRPF-NTVFQSYALFPHLTVFDNVAFGLKMAGVDVQ 111

Query: 135 DEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 194
           D AV +A+  L  V L E     P QLSGGQ+QRVAIARA+   P ++L DE  SALD +
Sbjct: 112 DIAVRVADA-LAIVRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYK 170

Query: 195 LVGEVLSVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQS 253
           L  ++   +K L    G+T + VTH+   A  +SD+I+ M+ G+ ++ G P+E++E P++
Sbjct: 171 LRQQMQLELKQLQRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRN 230

Query: 254 PRLAEFL 260
             +A+F+
Sbjct: 231 LFVAQFI 237


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: 369
Length adjustment: 27
Effective length of query: 238
Effective length of database: 342
Effective search space:    81396
Effective search space used:    81396
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.

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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