GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Lactobacillus silagei IWT126

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate WP_089136315.1 CES79_RS03445 ABC transporter permease subunit

Query= reanno::pseudo6_N2E2:Pf6N2E2_2959
         (242 letters)



>NCBI__GCF_002217945.1:WP_089136315.1
          Length = 479

 Score =  102 bits (253), Expect = 2e-26
 Identities = 71/211 (33%), Positives = 109/211 (51%), Gaps = 20/211 (9%)

Query: 25  QGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLI---RGVPDLVLMLL 81
           Q  W+T+     + L  V++GLLG           +    L TTLI   RG+P LVL L 
Sbjct: 283 QTVWLTVVAIFFATLFGVIVGLLGVVPN-------KFFNGLSTTLIYIFRGLPLLVLALF 335

Query: 82  IFYSLQTWLTSLTDFMEWEYIEIDPFGAGVITLGFIYGAYFTETFRGAILSVPRGQVEAA 141
           I+    T + SLT        +I  F AG ITL F  GAY     +G I +V  GQ+EAA
Sbjct: 336 IY----TGIPSLTGS------KIPAFVAGTITLMFNEGAYIAAFVKGGINAVDDGQMEAA 385

Query: 142 TAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKAAQDAGKST 201
            + GL  G+  R ++ PQ +R  +P   N +++ LK T+++SIIG+ +L +  +      
Sbjct: 386 RSLGLPFGKSMRRIILPQGIRIMIPSFINQFIITLKDTSILSIIGIIELTQTGKIIIARN 445

Query: 202 YQLFYFLVLAALIYLLITSASNFILRWLERR 232
            + F    + A+IYL++ +   ++  W+ERR
Sbjct: 446 LEGFKVWTIIAIIYLIVITLLTWLSNWVERR 476


Lambda     K      H
   0.329    0.142    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: 246
Number of extensions: 8
Number of successful extensions: 1
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: 242
Length of database: 479
Length adjustment: 28
Effective length of query: 214
Effective length of database: 451
Effective search space:    96514
Effective search space used:    96514
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: 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