GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Methylocystis bryophila S285

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_085772365.1 B1812_RS15290 ATP-binding cassette domain-containing protein

Query= reanno::Phaeo:GFF1302
         (334 letters)



>NCBI__GCF_002117405.1:WP_085772365.1
          Length = 257

 Score =  146 bits (368), Expect = 6e-40
 Identities = 90/246 (36%), Positives = 134/246 (54%), Gaps = 9/246 (3%)

Query: 4   IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63
           IKL+ V+K++  + V+  + LT+  G  T  +G SG GKSTLL LI GLE    G +RI 
Sbjct: 2   IKLDKVSKSYDALRVLDDVSLTLAQGCTTAVMGLSGSGKSTLLALIVGLEAPDQGEVRI- 60

Query: 64  GEDATNIPPA-----KRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAA 118
           G+D   + PA     +R +  V Q   L+PH++ R+NI    +  G  A  + +R+    
Sbjct: 61  GDD--RMAPASALNLRRRMGYVIQDGGLFPHLTARRNIELMSRELGWRAARRSKRLQELC 118

Query: 119 AALNL-TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEIS 177
                  + L+R P +LSGGQRQRV++ RA++ +P   L DEPL  LD   R  ++ ++ 
Sbjct: 119 TLTRFPAEALERYPAELSGGQRQRVSLMRALMLDPPILLLDEPLGALDPMTRARLQEDLK 178

Query: 178 ELHKRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSP 237
            + + L  T++ VTHD  EA  + D IV L  G + Q GS  +L  AP + F+  FI + 
Sbjct: 179 SIFRTLKKTVVIVTHDVSEAAFLGDTIVFLHQGRVLQQGSFRDLIAAPADPFITEFIRAQ 238

Query: 238 KMNLLT 243
              L T
Sbjct: 239 ASRLAT 244


Lambda     K      H
   0.320    0.138    0.400 

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: 189
Number of extensions: 7
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: 334
Length of database: 257
Length adjustment: 26
Effective length of query: 308
Effective length of database: 231
Effective search space:    71148
Effective search space used:    71148
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