GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Amycolatopsis halophila YIM 93223

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate WP_034276209.1 AMYHA_RS07110 ABC transporter ATP-binding protein

Query= TCDB::P0A9S7
         (255 letters)



>NCBI__GCF_000504245.1:WP_034276209.1
          Length = 257

 Score =  204 bits (520), Expect = 1e-57
 Identities = 101/245 (41%), Positives = 162/245 (66%), Gaps = 2/245 (0%)

Query: 10  GLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLRDQHL 69
           G+ + FGG+ A+++V+L++ P +++ +IGPNGAGKTT+FN   GF +P  GT+  RD+ L
Sbjct: 3   GINVNFGGIAALSDVSLDVAPNQVLGVIGPNGAGKTTLFNVACGFVQPDTGTLTWRDREL 62

Query: 70  EGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRRAQSE 129
           + L   Q+A +G+ RT Q + LF  MTV+EN++V   +  + G FSGLL  P   + +  
Sbjct: 63  KRLRPHQLAGLGIGRTLQGLGLFDRMTVLENVIVGADRHARAGFFSGLLGLPRSAKEERA 122

Query: 130 ALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGLNPKET 189
             DRA   L+ +G  +HA +  S+L Y  ++R+ +AR +V++P++L+LDEPAAGL+  + 
Sbjct: 123 LRDRAMALLDELGAAKHAGQLPSSLPYPVRKRVALARALVSEPDLLLLDEPAAGLSGDDM 182

Query: 190 KELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIRNNPDVIR 249
            EL ELI  L      +++L+EH M LVM + D I V++ G  +A+G P+Q++ +P V+ 
Sbjct: 183 AELGELIRGL--SRRMSVMLVEHHMDLVMSVCDHIVVLDFGKNIASGPPQQVKEDPAVLA 240

Query: 250 AYLGE 254
           AYLG+
Sbjct: 241 AYLGD 245


Lambda     K      H
   0.320    0.137    0.395 

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: 199
Number of extensions: 8
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: 255
Length of database: 257
Length adjustment: 24
Effective length of query: 231
Effective length of database: 233
Effective search space:    53823
Effective search space used:    53823
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 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