GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Halococcus hamelinensis 100A6

Align ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized)
to candidate WP_007695789.1 C447_RS16065 carbohydrate ABC transporter permease

Query= reanno::WCS417:GFF4322
         (281 letters)



>NCBI__GCF_000336675.1:WP_007695789.1
          Length = 305

 Score =  173 bits (439), Expect = 4e-48
 Identities = 106/292 (36%), Positives = 162/292 (55%), Gaps = 24/292 (8%)

Query: 8   PAISLSRIAIYAVLILAVLLYLVPLVVMLLTSFKTPEDISSGNLLSWPTV---VTGIGWV 64
           P   LSR  +Y +++  V  +LVPL   L+T+FKT + +++  L  +P +    T   WV
Sbjct: 15  PGFDLSRALLYLLILFFVAFFLVPLETGLMTAFKTTQGVTN-TLPFFPPLGEAFTFQKWV 73

Query: 65  KAWATVDGYFWNSIKITVPAVLISTAIGALNGYVLSFWRFKGSQLFFGLLLFGCFLPFQT 124
            A+  +     NS+ +TVPA L+    G+   Y L+   ++G      L L G F+P+Q 
Sbjct: 74  DAFDMLGRGLVNSMVLTVPATLLCLLFGSTAAYGLTLINWRGQIFVLVLFLIGIFIPYQA 133

Query: 125 VLLPASFTLGKMGLA----------------STTTGLVFVHVVYGLAFTTLFFRNYYVSI 168
           VL+P S     + L                 +    L+     YG+   TL FR YY+S+
Sbjct: 134 VLVPLSRFWSMVPLEEWLSPLYVLSFVQPEHAQLVELIITDAAYGIPICTLLFRGYYLSL 193

Query: 169 PDALIKAARLDGAGFFTIFRQIILPMSTPIIMVCLIWQFTQIWNDFLFGV-VFSSGDS-- 225
           P  LI+AA+LDGA   +I+R+I+LP+STP+I V  I+QFTQIWN+FLF + +  S DS  
Sbjct: 194 PGDLIEAAKLDGASVTSIYRRIVLPLSTPMIGVVFIYQFTQIWNEFLFTLTIVGSADSPA 253

Query: 226 QPITVALNNLVNTSTGAKEYNVDMAAAMIAGLPTLLVYVIAGKYFVRGLTAG 277
            P+T+ L+ L ++ +G  ++ + MA A IA LPTL++YV+  + F  GL  G
Sbjct: 254 APVTLILSGLGSSLSGV-DFGMRMAGAFIAALPTLVIYVLFAEQFAEGLETG 304


Lambda     K      H
   0.328    0.141    0.435 

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: 229
Number of extensions: 13
Number of successful extensions: 4
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: 281
Length of database: 305
Length adjustment: 26
Effective length of query: 255
Effective length of database: 279
Effective search space:    71145
Effective search space used:    71145
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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