GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluB in Kocuria turfanensis HO-9042

Align GluB aka CGL1951, component of Glutamate porter (characterized)
to candidate WP_062734864.1 AYX06_RS05070 glutamate ABC transporter substrate-binding protein

Query= TCDB::P48242
         (295 letters)



>NCBI__GCF_001580365.1:WP_062734864.1
          Length = 282

 Score =  197 bits (502), Expect = 2e-55
 Identities = 120/262 (45%), Positives = 158/262 (60%), Gaps = 21/262 (8%)

Query: 18  ALAGVTLTACGDSSGGDGFLAAIENG----SVNVGTKYDQPGLGLRNPDNSMSGLDVDVA 73
           A A +TLTACG   GG       E G    SV +G KYDQPGLG R+ D   +G DVDVA
Sbjct: 14  AAAALTLTACG---GGGEQAGGGETGGSGESVRIGIKYDQPGLGFRDGDQ-YTGFDVDVA 69

Query: 74  EYVVNSIADDKGWDHPTIEWRESPSAQRETLIQNGEVDMIAATYSINAGRSESVNFGGPY 133
           +YV N +    G+    IEW ESPSA RE ++ N +VDMI ATYSI   R ++V+F GPY
Sbjct: 70  KYVANEL----GYAEDQIEWVESPSANRENMLANDQVDMIFATYSITEERDQTVDFAGPY 125

Query: 134 LLTHQALLVRQDDDRIETLEDLDNGLILCSVSGSTPAQKVKDVLPGVQLQEYDTYSSCVE 193
            +  Q LLVR DD  I   +DL+ G  LCSV+GST AQKVK+  PG  L E   Y+ C+ 
Sbjct: 126 FVAGQDLLVRSDDTSITGPDDLE-GKNLCSVTGSTSAQKVKEDQPGANLVEQPGYADCLT 184

Query: 194 ALSQGNVDALTTDATILFGY--SQQYEGDFRVVEMEKDGEPFTDEYYGIGLKKDDQEGTD 251
           AL  G VDA+TTD  IL G   ++  +G F+VV     G  F++E YG+GL +   +  +
Sbjct: 185 ALESGQVDAVTTDDIILAGLAATEANQGKFKVV-----GNTFSEERYGVGLPQGSDQ-CE 238

Query: 252 AINAALERMYADGTFQRLLTEN 273
           A+N A+ +M  +G ++  +T N
Sbjct: 239 AVNEAITKMIDEGAWEEAVTAN 260


Lambda     K      H
   0.312    0.133    0.378 

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: 273
Number of extensions: 21
Number of successful extensions: 5
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: 295
Length of database: 282
Length adjustment: 26
Effective length of query: 269
Effective length of database: 256
Effective search space:    68864
Effective search space used:    68864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (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