GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluC in Dietzia timorensis ID05-A0528

Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate WP_067473904.1 BJL86_RS10995 amino acid ABC transporter permease

Query= TCDB::P48244
         (228 letters)



>NCBI__GCF_001659785.1:WP_067473904.1
          Length = 224

 Score =  300 bits (767), Expect = 2e-86
 Identities = 155/225 (68%), Positives = 185/225 (82%), Gaps = 1/225 (0%)

Query: 4   LWADLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTP 63
           +W + GP+L PAFW+TIKLT +SAIG++I+GTILT +RV PV ILR  S AY+N VRNTP
Sbjct: 1   MWEEFGPALWPAFWMTIKLTFFSAIGSLIWGTILTALRVCPVPILRGFSAAYVNIVRNTP 60

Query: 64  LTLVVLFCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTV 123
           LTLVVLFCS GLYQNLGL LA  E+  F+ +NNF LAVL FILYTSTFV E+LRSGINTV
Sbjct: 61  LTLVVLFCSMGLYQNLGLALAP-ENDHFIENNNFNLAVLAFILYTSTFVCETLRSGINTV 119

Query: 124 HFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASLL 183
             GQAEAARSLGLGFG     I+ PQA R+ I PL + LIAL KNTTIASVIGV EASLL
Sbjct: 120 PMGQAEAARSLGLGFGQILGLIVLPQAFRSVINPLASVLIALIKNTTIASVIGVAEASLL 179

Query: 184 MKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERLAVKK 228
           MK+TIE++A  L+V+FA+ A+GF+ILTLP+GL LGK+SE++AVK+
Sbjct: 180 MKSTIESYAGDLYVIFAVIALGFVILTLPVGLLLGKVSEKVAVKR 224


Lambda     K      H
   0.327    0.139    0.397 

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: 260
Number of extensions: 9
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: 228
Length of database: 224
Length adjustment: 22
Effective length of query: 206
Effective length of database: 202
Effective search space:    41612
Effective search space used:    41612
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 (21.7 bits)
S2: 46 (22.3 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