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_078211033.1 BXU11_RS03565 ABC transporter ATP-binding protein

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



>NCBI__GCF_002017945.1:WP_078211033.1
          Length = 233

 Score =  155 bits (393), Expect = 5e-43
 Identities = 89/233 (38%), Positives = 137/233 (58%), Gaps = 11/233 (4%)

Query: 14  IIQMQGVNKWY----GQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQG 69
           +I+++ ++K Y     + HVLK IN N+K+GE + + G SGSGKST +  L  L+E   G
Sbjct: 1   MIEIKDLHKSYKMGSSELHVLKGINFNIKEGELVAIMGSSGSGKSTLLNILGILDEADSG 60

Query: 70  RIVVDGVELTNDLKQIEAIRRE--VGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAE 127
             ++D V +    + I +  R   +G VFQ FNL  + T L N  + P++ + + +++  
Sbjct: 61  SYILDTVPIKKLNETIASKYRNQFLGFVFQSFNLINYKTALDNVAM-PLYYQGIKRKERN 119

Query: 128 EIAMHYLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKE 187
           EIAM YL +V +   +H  P +LSGGQ+QRVAIARAL   PK++L DEPT ALD +   E
Sbjct: 120 EIAMKYLGKVGLATHSHHLPNELSGGQKQRVAIARALASNPKVLLADEPTGALDTKTSYE 179

Query: 188 VLDTMIGLAEDGMTMLCVTHEMGFARTVANRVIFMD----KGEIVEQAAPNDF 236
           V++ + G+ ++G T+L VTHE   A      V+  D      ++VEQ   + +
Sbjct: 180 VMELIQGINDEGKTILIVTHEPDIAAMCKRNVVLKDGLIIDDKLVEQVRASSY 232


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: 141
Number of extensions: 5
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: 233
Length adjustment: 23
Effective length of query: 231
Effective length of database: 210
Effective search space:    48510
Effective search space used:    48510
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