GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Nocardiopsis baichengensis YIM 90130

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_017557172.1 C892_RS0110655 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_000341205.1:WP_017557172.1
          Length = 281

 Score =  124 bits (311), Expect = 2e-33
 Identities = 81/248 (32%), Positives = 132/248 (53%), Gaps = 16/248 (6%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           +L V+ L VA+GG+ A+  V F+V    +V LIG NGAGKTT   A++G +    G +  
Sbjct: 7   VLAVEQLTVAFGGLTALDRVTFDVPHRSVVGLIGPNGAGKTTVFNAVSGVVRPRSGTLTR 66

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGA--YIRKDKAGILADIEKMF 126
            G+ ++      L + G+  + +G G+F+ MT+ EN+ +GA         G+L  + +  
Sbjct: 67  HGRPLRRHRPHHLPRLGISRMLQGLGLFSGMTVLENVMVGADPLATGRLPGMLTGLGRAP 126

Query: 127 TIFPRLRERKDQ-------------LAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGL 173
               R+RER +              L GT+  G Q+ +A+ RA +  P++LLLDEP+ GL
Sbjct: 127 RDERRVRERAESALREFGVAHAAHALPGTLPYGVQKRVALARACVCGPELLLLDEPASGL 186

Query: 174 SPIMVDKIFEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDP 233
           S   + ++ E VR + A G +++LVE +    + + DR  V++ G +   G   ++  DP
Sbjct: 187 SADEMSELAERVRAMRAYG-SVLLVEHHMDLVMRVCDRVVVLDFGRVIADGTPDEVRADP 245

Query: 234 KVRAAYLG 241
            V  AYLG
Sbjct: 246 AVERAYLG 253


Lambda     K      H
   0.317    0.136    0.373 

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: 173
Number of extensions: 16
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: 242
Length of database: 281
Length adjustment: 25
Effective length of query: 217
Effective length of database: 256
Effective search space:    55552
Effective search space used:    55552
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: 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