GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Flavobacterium sp. LM5

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_024980276.1 BXU11_RS09570 ABC transporter ATP-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>NCBI__GCF_002017945.1:WP_024980276.1
          Length = 228

 Score =  130 bits (326), Expect = 3e-35
 Identities = 82/202 (40%), Positives = 113/202 (55%), Gaps = 4/202 (1%)

Query: 28  HVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVVDGVELTN--DLKQI 85
           +VLK I+L + +GE + L GPSGSGKST +  L  L+    G  +++G +++   D +  
Sbjct: 23  YVLKGIDLEINKGEYVALMGPSGSGKSTLMNLLGCLDTPTSGTYILNGKDVSKMKDDELA 82

Query: 86  EAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHYLERVRIPEQAHK 145
           E   +E+G VFQ FNL P  T L N  L PM      K +    A   L +V + ++   
Sbjct: 83  EIRNKEIGFVFQTFNLLPRTTALDNVAL-PMIYAGHSKTERTTRATEVLNQVNLGDRMDH 141

Query: 146 YPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMIGLAEDGMTMLCV 205
            P QLSGGQ+QRVAIARAL  KP I+L DEPT  LD +   E++     +   G T++ V
Sbjct: 142 QPNQLSGGQRQRVAIARALVNKPSIILADEPTGNLDSKTSVEIMKLFGDIHAQGNTVILV 201

Query: 206 THEMGFARTVANRVIFMDKGEI 227
           THE   A   A+RVI +  G I
Sbjct: 202 THEEDIA-AYAHRVIRLRDGLI 222


Lambda     K      H
   0.322    0.137    0.407 

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: 128
Number of extensions: 6
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: 254
Length of database: 228
Length adjustment: 23
Effective length of query: 231
Effective length of database: 205
Effective search space:    47355
Effective search space used:    47355
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. 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