GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Methylocystis bryophila S285

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_085772469.1 B1812_RS15935 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_002117405.1:WP_085772469.1
          Length = 254

 Score = 93.6 bits (231), Expect = 4e-24
 Identities = 80/252 (31%), Positives = 120/252 (47%), Gaps = 33/252 (13%)

Query: 6   MTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTV 65
           M+ TP L V+ L+  +G   A++DVS     G    ++G NGAGK+TLF+  TG Y    
Sbjct: 1   MSETPALNVKSLSHAYGARKALDDVSLRVERGAFAVLLGLNGAGKSTLFSLATGLYGARA 60

Query: 66  GRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRAS 125
           G + +   D     + + PG  + +   V   FQ   L   +S+ +NL+           
Sbjct: 61  GAVEIMGYD-----VAKTPGEALRRLGVV---FQARTLDLELSLTQNLLYH--------- 103

Query: 126 GFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCT 185
               A L G+        E   LA   L+R  L E A  +A +L  G  RR+EIARA+  
Sbjct: 104 ----AALHGI-----GPGEGKRLAGAALERAGLSERAREKARDLSGGQMRRVEIARALLH 154

Query: 186 EPVMLCLDEPAAGLNPRESGELADLLTYIRD---EHKIGVLLIEHDMSVVMTISDHVVVL 242
            P +L LDEP  GL+ +     AD+L ++R    +  + VL   H +  +   SD V++L
Sbjct: 155 RPSLLLLDEPTVGLDIKAR---ADILKHVRGLVAQENLAVLWTTHLIDEIAP-SDQVIML 210

Query: 243 DYGRKISDGDPA 254
             GR ++DG  A
Sbjct: 211 HEGRVLTDGSAA 222


Lambda     K      H
   0.319    0.137    0.397 

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: 163
Number of extensions: 9
Number of successful extensions: 2
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: 294
Length of database: 254
Length adjustment: 25
Effective length of query: 269
Effective length of database: 229
Effective search space:    61601
Effective search space used:    61601
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: 47 (22.7 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