GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Nocardiopsis gilva YIM 90087

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_017616633.1 CDO52_RS13840 carbohydrate ABC transporter permease

Query= uniprot:A8LLL4
         (385 letters)



>NCBI__GCF_002263495.1:WP_017616633.1
          Length = 315

 Score =  227 bits (578), Expect = 4e-64
 Identities = 111/233 (47%), Positives = 158/233 (67%), Gaps = 7/233 (3%)

Query: 153 PPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRA 212
           P   T  NY  +L    ++EG   +FFNT+ +++P+T++ +++AA AAYA AWMEFPGR 
Sbjct: 90  PSRLTLENYAGLL----DNEGFVASFFNTILISVPSTVLIVVIAALAAYAFAWMEFPGRD 145

Query: 213 LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGL 272
            L   +VGLLVVPLQ+ALIP+  ++  +GI     G  L H GFG+P AI+LLRN+   +
Sbjct: 146 WLFLGVVGLLVVPLQVALIPIAQVYGPLGIYGSIPGVVLFHVGFGLPFAIFLLRNFFAAI 205

Query: 273 PRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQT 332
           PRD++E A++DG  +  IF +++LPL  PA+AS AIFQFLW WNDLLVA VF   A    
Sbjct: 206 PRDLLEAARMDGGKELTIFRRVILPLGGPAIASLAIFQFLWVWNDLLVALVFADSANQPM 265

Query: 333 TVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385
           TV     +      G N +++++ AF+S+ VPLLVFF+ QR+ V+G++AG+VK
Sbjct: 266 TVALQSEMRQF---GANIDVISSGAFLSMVVPLLVFFAFQRYFVQGVMAGAVK 315



 Score = 47.4 bits (111), Expect = 6e-10
 Identities = 20/40 (50%), Positives = 29/40 (72%)

Query: 14 AVQLSVVGLVVLWLLPTFGLFVSSFRTVEQISSSGWWKAM 53
          A+Q+ +V + + WLLPT GLFVSS R+ +  +SSGWW  +
Sbjct: 48 AIQVLLVLVGLFWLLPTLGLFVSSLRSPQDNASSGWWTVL 87


Lambda     K      H
   0.323    0.138    0.419 

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: 330
Number of extensions: 16
Number of successful extensions: 3
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: 385
Length of database: 315
Length adjustment: 29
Effective length of query: 356
Effective length of database: 286
Effective search space:   101816
Effective search space used:   101816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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