GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Croceitalea dokdonensis DOKDO 023

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_054557498.1 I595_RS00860 ABC transporter ATP-binding protein

Query= CharProtDB::CH_024626
         (378 letters)



>NCBI__GCF_001306415.1:WP_054557498.1
          Length = 219

 Score =  132 bits (333), Expect = 7e-36
 Identities = 75/220 (34%), Positives = 126/220 (57%), Gaps = 10/220 (4%)

Query: 17  LVQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGR--- 73
           ++    I+K +   +V+  + ++I  GE ++++GPSG GKTT+L+L+  L+T  + +   
Sbjct: 1   MITATNIKKNYGDLKVLKGVSISIKKGEVISIVGPSGAGKTTLLQLVGTLDTPSNPKDSS 60

Query: 74  IMLDNEDITHVPAE------NRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPR 127
           IM++  D+T +  +      N  +  +FQ + L P  T  ENV     ++KTP A+   R
Sbjct: 61  IMINGVDVTDLRDKQLAKFRNENIGFIFQFHQLLPEFTALENVCIPAFIKKTPKAKAEVR 120

Query: 128 VMEALRMVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQ 187
             E L  + L      +P +LSGG+QQRVA+ARA++N P ++  DE    LD +  + + 
Sbjct: 121 GRELLDFLGLSQRYDHRPRELSGGEQQRVAVARALINNPSVIFADEPSGNLDSESAENLH 180

Query: 188 NELKALQRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIE 227
                L+ + G TFV VTH++E A  M+DR ++M DG+I+
Sbjct: 181 QLFFKLREEFGQTFVIVTHNKELA-NMADRKLIMVDGQIQ 219


Lambda     K      H
   0.319    0.136    0.385 

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: 191
Number of extensions: 8
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: 378
Length of database: 219
Length adjustment: 26
Effective length of query: 352
Effective length of database: 193
Effective search space:    67936
Effective search space used:    67936
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 (21.7 bits)
S2: 47 (22.7 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