GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Alkalihalobacterium alkalinitrilicum DSM 22532

Align BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= TCDB::Q93A35
         (328 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  192 bits (489), Expect = 8e-54
 Identities = 107/240 (44%), Positives = 150/240 (62%), Gaps = 8/240 (3%)

Query: 2   IRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIY 61
           I+FDNV+K Y+   T AV+ + L+I +GE    +GPSGCGKTTTL+M+      TTG I 
Sbjct: 4   IQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTGKIR 63

Query: 62  INEKRISDYDIHEL---RWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITE 118
           I ++ + D D   L   +  IG V Q  ALFPH+TIE+N+     L +W       R  E
Sbjct: 64  IGDEVVYD-DRRALPPEKRGIGMVFQDYALFPHLTIEKNVTF--GLNRWKNRDKKKRAQE 120

Query: 119 LLDSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQ 178
           +L+ VGL    + HR P+ELSGG+QQRV + RALA  P +ILMDEPFS LD   R++++ 
Sbjct: 121 VLELVGLG--EFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178

Query: 179 DISALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFL 238
           D++ + +K   T + VTHD ++A A+ DR+ VM  G I Q+A P+E+ + P N FV  F+
Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238


Lambda     K      H
   0.318    0.136    0.386 

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: 299
Number of extensions: 10
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: 328
Length of database: 351
Length adjustment: 28
Effective length of query: 300
Effective length of database: 323
Effective search space:    96900
Effective search space used:    96900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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