GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02872 in Nocardiopsis gilva YIM 90087

Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate WP_152471781.1 CDO52_RS22265 ABC transporter permease subunit

Query= reanno::Smeli:SMc02872
         (315 letters)



>NCBI__GCF_002263495.1:WP_152471781.1
          Length = 265

 Score =  193 bits (491), Expect = 3e-54
 Identities = 109/256 (42%), Positives = 149/256 (58%), Gaps = 6/256 (2%)

Query: 55  QLTFVGLGNFKVLFGDPRWAADFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKLRFG 114
           +L F GL NF  LF    +    W A  +N  FF   M VQ  +G+A A +L     R G
Sbjct: 9   RLGFAGLDNFAHLFSGV-YGDRLWRAFGHNLAFFAGTMLVQTTLGLAFAVLLR--HTRAG 65

Query: 115 A-FYRTAIFLPTLLSFVIVGFIWKLILSPIWGVAPYLLDTVGLRSLFGPWLGKPDTALIA 173
             F +TA  LP L+S ++VG++W L+LSP +G     L  VGL +L  PW G P  AL  
Sbjct: 66  RRFLQTAYVLPHLVSPIVVGYLWSLMLSPQFGAVNAALRAVGLDALAQPWTGDPALALPT 125

Query: 174 VSLISVWQYIGIPMMLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGIVSI 233
           + L++ WQ+IG PM+L  AAL  IP E  EAA +DG +GW  F  + LPL++PAIGIV++
Sbjct: 126 LILVNAWQWIGFPMLLFSAALAGIPPEYEEAARVDGASGWQAFRTVTLPLLMPAIGIVTV 185

Query: 234 LTFVGNFNAFDLIYTVQGALAGPDKSTDILGTLLYRTFFGFQLQLGDRSMGATIAAIMFL 293
           LTF+GN N  DL+Y +QG+   P  +TD+LG L YRT F      G     + +A +MF+
Sbjct: 186 LTFIGNMNVLDLVYAMQGSQGAPAGATDVLGLLFYRTAFN-NPDPGAIGQASALAVVMFV 244

Query: 294 IILAGVALYLFGIQRR 309
            I  GV++    + RR
Sbjct: 245 FIF-GVSIAATRVLRR 259


Lambda     K      H
   0.331    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: 318
Number of extensions: 17
Number of successful extensions: 2
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: 315
Length of database: 265
Length adjustment: 26
Effective length of query: 289
Effective length of database: 239
Effective search space:    69071
Effective search space used:    69071
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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