GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0326 in Halococcus hamelinensis 100A6

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate WP_007695789.1 C447_RS16065 carbohydrate ABC transporter permease

Query= TCDB::Q72KX4
         (268 letters)



>NCBI__GCF_000336675.1:WP_007695789.1
          Length = 305

 Score =  187 bits (474), Expect = 3e-52
 Identities = 112/289 (38%), Positives = 157/289 (54%), Gaps = 28/289 (9%)

Query: 1   MGRALLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFR-----TA 55
           + RALLY  +L    FFL+P+   ++TA K    +T    +    PP  E+F       A
Sbjct: 19  LSRALLYLLILFFVAFFLVPLETGLMTAFKTTQGVTNTLPF---FPPLGEAFTFQKWVDA 75

Query: 56  WEAFRPKFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSIL 115
           ++       NS+VL V ATLL  L GS   Y L    +RG   +  L L G+FIPYQ++L
Sbjct: 76  FDMLGRGLVNSMVLTVPATLLCLLFGSTAAYGLTLINWRGQIFVLVLFLIGIFIPYQAVL 135

Query: 116 IPLFQFMKSIGL----------------YGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPD 159
           +PL +F   + L                +  L  L++    YGIPI TL+FR YY  +P 
Sbjct: 136 VPLSRFWSMVPLEEWLSPLYVLSFVQPEHAQLVELIITDAAYGIPICTLLFRGYYLSLPG 195

Query: 160 ELVEAARIDGAGFFGIFRHVILPLSVPAFVVVAIWQFTQIWNEFLFAVTL---TRPESQP 216
           +L+EAA++DGA    I+R ++LPLS P   VV I+QFTQIWNEFLF +T+       + P
Sbjct: 196 DLIEAAKLDGASVTSIYRRIVLPLSTPMIGVVFIYQFTQIWNEFLFTLTIVGSADSPAAP 255

Query: 217 ITVALAQLAGG-EAVKWNLPMAGAILAALPTLLVYILLGRYFLRGLLAG 264
           +T+ L+ L      V + + MAGA +AALPTL++Y+L    F  GL  G
Sbjct: 256 VTLILSGLGSSLSGVDFGMRMAGAFIAALPTLVIYVLFAEQFAEGLETG 304


Lambda     K      H
   0.330    0.146    0.461 

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: 284
Number of extensions: 17
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: 268
Length of database: 305
Length adjustment: 26
Effective length of query: 242
Effective length of database: 279
Effective search space:    67518
Effective search space used:    67518
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: 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