GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Halopiger salifodinae KCY07-B2

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_049991787.1 LT39_RS17480 carbohydrate ABC transporter permease

Query= uniprot:A8LLL4
         (385 letters)



>NCBI__GCF_000784335.1:WP_049991787.1
          Length = 288

 Score = 99.8 bits (247), Expect = 9e-26
 Identities = 66/209 (31%), Positives = 114/209 (54%), Gaps = 8/209 (3%)

Query: 180 NTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHNA 239
           NT+ +    TI+ +L+ A  AY+L  +++PGR  + A+IV   +VP  + L+P+  + + 
Sbjct: 85  NTVILAGVTTIVVMLIDAMIAYSLTRLDWPGRRAIFAVIVASFMVPGIVNLVPVYIIVSE 144

Query: 240 IGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLPLS 299
           +G+     G  L       PL +++L  +   +P ++ E A++DG +  ++F+ IVLPL 
Sbjct: 145 LGLVNSVWGVVLPSAA--NPLGVFMLVQFFKDIPEELEEAARLDGFSRLRVFSHIVLPLM 202

Query: 300 FPALASFAIFQFLWTWNDLL-VAKVFLIDATGQTTVMTNQIVELLG-TRGGNWEILATAA 357
             ALA+  +F F+WTWN  +    +F  DA     +    + + LG T  G   ++ T+A
Sbjct: 203 RSALAALGLFIFIWTWNAFVWPLLIFQDDAMYTLPIGLVTLQDNLGVTEPG---VIMTSA 259

Query: 358 FVSIAVPLLVFFSMQRFLVRGL-LAGSVK 385
            V+    LLVF  MQ+ LVR + + G+ K
Sbjct: 260 VVASVPLLLVFLVMQKHLVRAVEMQGTTK 288


Lambda     K      H
   0.323    0.138    0.419 

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: 267
Number of extensions: 13
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: 385
Length of database: 288
Length adjustment: 28
Effective length of query: 357
Effective length of database: 260
Effective search space:    92820
Effective search space used:    92820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 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