GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Nocardiopsis gilva YIM 90087

Align GtsC (GLcG), component of Glucose porter, GtsABCD (characterized)
to candidate WP_017616633.1 CDO52_RS13840 carbohydrate ABC transporter permease

Query= TCDB::Q88P36
         (281 letters)



>NCBI__GCF_002263495.1:WP_017616633.1
          Length = 315

 Score =  155 bits (393), Expect = 8e-43
 Identities = 96/273 (35%), Positives = 157/273 (57%), Gaps = 13/273 (4%)

Query: 16  AIHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGN---LLSWPAVIT---GIGWVKAWGA 69
           AI  +L++  L +L+P + + ++S ++P+D  +     +L+ P+ +T     G +   G 
Sbjct: 48  AIQVLLVLVGLFWLLPTLGLFVSSLRSPQDNASSGWWTVLAAPSRLTLENYAGLLDNEGF 107

Query: 70  VSGYFWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPA 129
           V+ +F N+I+I+VP+ ++   I AL  Y  +   F G    F  ++    +P Q  L+P 
Sbjct: 108 VASFF-NTILISVPSTVLIVVIAALAAYAFAWMEFPGRDWLFLGVVGLLVVPLQVALIPI 166

Query: 130 SFTLGKLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKAARLDGAGFFTIFRR 189
           +   G LG+  +  G+VL HV +GL F     RNF+ +IP  L++AAR+DG    TIFRR
Sbjct: 167 AQVYGPLGIYGSIPGVVLFHVGFGLPFAIFLLRNFFAAIPRDLLEAARMDGGKELTIFRR 226

Query: 190 IILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNLVNTSTGAKEYNVDM 249
           +ILP+  P I    I+QF  +WND L  +VF+   +QP+TVAL + +    GA   N+D+
Sbjct: 227 VILPLGGPAIASLAIFQFLWVWNDLLVALVFADSANQPMTVALQSEMR-QFGA---NIDV 282

Query: 250 --AAAMIAGLPTLLVYVVAGKYFVRGLTAGAVK 280
             + A ++ +  LLV+    +YFV+G+ AGAVK
Sbjct: 283 ISSGAFLSMVVPLLVFFAFQRYFVQGVMAGAVK 315


Lambda     K      H
   0.329    0.142    0.443 

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: 226
Number of extensions: 9
Number of successful extensions: 3
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: 281
Length of database: 315
Length adjustment: 26
Effective length of query: 255
Effective length of database: 289
Effective search space:    73695
Effective search space used:    73695
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: 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