GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Polaromonas naphthalenivorans CJ2

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate WP_011803054.1 PNAP_RS18455 carbohydrate ABC transporter permease

Query= reanno::Smeli:SMc03063
         (380 letters)



>NCBI__GCF_000015505.1:WP_011803054.1
          Length = 289

 Score =  110 bits (274), Expect = 6e-29
 Identities = 70/220 (31%), Positives = 116/220 (52%), Gaps = 9/220 (4%)

Query: 162 GIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIP 221
           G+   F NS+++A+P+ +I     A   Y L+   F G  +L   ++  + +P Q+ L+P
Sbjct: 77  GLQPYFWNSVSMAIPAVLISTAWGAVNGYVLSLWKFRGSELLFGFLLFGVFMPFQVVLLP 136

Query: 222 LLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASD 281
           + Q+   +G    +      G+ L H   G+       RNY   +P+E++ +AR+DGA  
Sbjct: 137 MSQVLGYLGLSSSIG-----GLVLVHCLAGMAGTTLFFRNYYTAIPKELVNAARMDGAGF 191

Query: 282 FDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGG 341
           + IF +I+LPLS P L    I+QF   WND L  + F GA D K +  G L N+  +   
Sbjct: 192 WRIFWRIVLPLSTPILMVTLIWQFTNIWNDFLFGVAFSGA-DSKPITVG-LNNMANTSSS 249

Query: 342 --NWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379
             ++ +  A+A I  +  ++V+    +Y V+GL AG+VKG
Sbjct: 250 VKSYNVDMAAAVIAGLPTMLVYVLAGQYFVKGLTAGAVKG 289


Lambda     K      H
   0.324    0.139    0.418 

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: 247
Number of extensions: 10
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 380
Length of database: 289
Length adjustment: 28
Effective length of query: 352
Effective length of database: 261
Effective search space:    91872
Effective search space used:    91872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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