GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Nocardiopsis gilva YIM 90087

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate WP_017616633.1 CDO52_RS13840 carbohydrate ABC transporter permease

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



>NCBI__GCF_002263495.1:WP_017616633.1
          Length = 315

 Score =  238 bits (607), Expect = 2e-67
 Identities = 119/233 (51%), Positives = 167/233 (71%), Gaps = 7/233 (3%)

Query: 146 PPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLA 205
           P R TL+NYA +L   G   SF N++ ++VPSTV+ ++IAA AAYA AWM FPGR  L  
Sbjct: 90  PSRLTLENYAGLLDNEGFVASFFNTILISVPSTVLIVVIAALAAYAFAWMEFPGRDWLFL 149

Query: 206 VVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAG 265
            VVGLLVVPLQ++LIP+ Q+Y  +G +  +      G+ L H GFGLP AI+LLRN+ A 
Sbjct: 150 GVVGLLVVPLQVALIPIAQVYGPLGIYGSIP-----GVVLFHVGFGLPFAIFLLRNFFAA 204

Query: 266 LPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDK 325
           +PR+++E+AR+DG  +  IF ++ILPL  PA+AS AIFQFLW WNDLLVA+VF  + +  
Sbjct: 205 IPRDLLEAARMDGGKELTIFRRVILPLGGPAIASLAIFQFLWVWNDLLVALVFADSANQP 264

Query: 326 LVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVK 378
             +T  L + +   G N +++++ AF+++VVPL+VFFA QRY V+G++AG+VK
Sbjct: 265 --MTVALQSEMRQFGANIDVISSGAFLSMVVPLLVFFAFQRYFVQGVMAGAVK 315



 Score = 50.1 bits (118), Expect = 9e-11
 Identities = 22/45 (48%), Positives = 30/45 (66%)

Query: 12 AVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSR 56
          A+ + ++L+ L W LPT GL +SSLR     A SGWWT L++ SR
Sbjct: 48 AIQVLLVLVGLFWLLPTLGLFVSSLRSPQDNASSGWWTVLAAPSR 92


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: 299
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: 2
Length of query: 380
Length of database: 315
Length adjustment: 29
Effective length of query: 351
Effective length of database: 286
Effective search space:   100386
Effective search space used:   100386
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 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