GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Planococcus halocryophilus Or1

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_008497300.1 B481_RS06650 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_000342445.1:WP_008497300.1
          Length = 310

 Score =  112 bits (279), Expect = 1e-29
 Identities = 82/276 (29%), Positives = 134/276 (48%), Gaps = 26/276 (9%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           +LK E L+ KF   +A+++ + E  +G+   L+GPNGAGK+T  + I+   +PT G +  
Sbjct: 1   MLKTEKLTKKFKDTLAVDEVTIELGQGESVGLLGPNGAGKSTAISMISTLIQPTSGDVRL 60

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
           N KS    +L++  + R      +    Q I L+  L+  ENL         K  G  I 
Sbjct: 61  NGKS----VLKKPGEMRKV----LGVVPQKIALYEELSAYENL---------KFFG-RIY 102

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
           GL G     ++  E I++    LE   L DR  +       G QRR+ +A AM   PE+L
Sbjct: 103 GLSG-----KKLEERIQIV---LELVGLSDRQKELVKKYSGGMQRRVNLAAAMLHEPEVL 154

Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253
            +DEP  G++P+    L   ++ +  E G ++L   H M  V ++ D V ++++G+ I+ 
Sbjct: 155 IMDEPTVGIDPQSRNHLLETIRKLNREQGMTVLYTSHYMEEVEKLCDRVYIMDHGKVIAA 214

Query: 254 GTPDHVKNDPRVIAAYLGVEDEEVEEVIAAVEQLEG 289
           GT D +K         L   D+    +   + Q+EG
Sbjct: 215 GTKDELKGVLSEEETVLIEFDQNYPPLFEKISQMEG 250


Lambda     K      H
   0.318    0.136    0.386 

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: 176
Number of extensions: 5
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: 292
Length of database: 310
Length adjustment: 27
Effective length of query: 265
Effective length of database: 283
Effective search space:    74995
Effective search space used:    74995
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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