GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Amantichitinum ursilacus IGB-41

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_053937456.1 WG78_RS08860 amino acid ABC transporter permease

Query= TCDB::Q52665
         (434 letters)



>NCBI__GCF_001294205.1:WP_053937456.1
          Length = 221

 Score =  101 bits (252), Expect = 2e-26
 Identities = 70/230 (30%), Positives = 120/230 (52%), Gaps = 23/230 (10%)

Query: 206 AALQSALPLALPEVDSDQFGGFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVG 265
           A LQSA P  L         G+ L   +G  A+V  L +G LLA+ R S +  ++  +  
Sbjct: 5   ALLQSAWPYLLKGT------GYTLLFAVG--AMVGGLLVGALLAVLRLSGIKALQWPAAL 56

Query: 266 IIEFVRGVPLITLLFTASLLLQYFLPP-GTNFDLILRVVILVTLFAAAYIAEVIRGGLAA 324
            +  +RG PL+  +F    ++ Y LP  G  F+ I   ++ ++L   AY++E +RG +  
Sbjct: 57  YVSAMRGTPLLVQIF----IIYYGLPAIGIQFEPITAGILALSLNTGAYVSETMRGAING 112

Query: 325 LPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLK 384
           + RGQ+EAA + G+  WQ    I+ PQAL++++P + +S I L KDT+LV+ + + + + 
Sbjct: 113 VDRGQWEAAFSQGMGRWQTLHYIVWPQALRLAVPSLSNSLISLIKDTSLVSVIAVTELML 172

Query: 385 GISNVVRSDMAWKGTYWEP---YIFVALIFFLFNFSMSRYSMYLERKLKR 431
               V+        T ++P   Y+  A I++  +    +    LER+L R
Sbjct: 173 ATKEVI-------STTFQPFPLYVAAAAIYWCLSLIFEQVQRLLERRLGR 215


Lambda     K      H
   0.329    0.143    0.457 

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: 271
Number of extensions: 15
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: 434
Length of database: 221
Length adjustment: 27
Effective length of query: 407
Effective length of database: 194
Effective search space:    78958
Effective search space used:    78958
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