GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0326 in Polaromonas naphthalenivorans CJ2

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_011803054.1 PNAP_RS18455 carbohydrate ABC transporter permease

Query= TCDB::Q72KX4
         (268 letters)



>NCBI__GCF_000015505.1:WP_011803054.1
          Length = 289

 Score =  257 bits (657), Expect = 2e-73
 Identities = 133/279 (47%), Positives = 188/279 (67%), Gaps = 11/279 (3%)

Query: 1   MGRALLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEA-- 58
           + RALLY  LL+ A FFL P Y+++ T+ K+  +I    +   P    ++++R AW +  
Sbjct: 11  LSRALLYAVLLVAALFFLAPFYVMLATSFKDAEQIRSGNLLSPPASLNFDAWRLAWSSAC 70

Query: 59  -------FRPKFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPY 111
                   +P F NSV +A+ A L+S   G++NGYVL+ W FRGS LLF  +LFG+F+P+
Sbjct: 71  TGVDCRGLQPYFWNSVSMAIPAVLISTAWGAVNGYVLSLWKFRGSELLFGFLLFGVFMPF 130

Query: 112 QSILIPLFQFMKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAG 171
           Q +L+P+ Q +  +GL  S+ GLVLVH + G+   TL FRNYY+ IP ELV AAR+DGAG
Sbjct: 131 QVVLLPMSQVLGYLGLSSSIGGLVLVHCLAGMAGTTLFFRNYYTAIPKELVNAARMDGAG 190

Query: 172 FFGIFRHVILPLSVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQPITVALAQLAG-GEAV 230
           F+ IF  ++LPLS P  +V  IWQFT IWN+FLF V  +  +S+PITV L  +A    +V
Sbjct: 191 FWRIFWRIVLPLSTPILMVTLIWQFTNIWNDFLFGVAFSGADSKPITVGLNNMANTSSSV 250

Query: 231 K-WNLPMAGAILAALPTLLVYILLGRYFLRGLLAGSVKG 268
           K +N+ MA A++A LPT+LVY+L G+YF++GL AG+VKG
Sbjct: 251 KSYNVDMAAAVIAGLPTMLVYVLAGQYFVKGLTAGAVKG 289


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: 309
Number of extensions: 10
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: 289
Length adjustment: 25
Effective length of query: 243
Effective length of database: 264
Effective search space:    64152
Effective search space used:    64152
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 Apr 09 2024. 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