GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Rhodococcus qingshengii djl-6-2

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_003940114.1 C1M55_RS25960 ATP-binding cassette domain-containing protein

Query= TCDB::Q93A35
         (328 letters)



>NCBI__GCF_002893965.1:WP_003940114.1
          Length = 371

 Score =  229 bits (583), Expect = 1e-64
 Identities = 138/315 (43%), Positives = 189/315 (60%), Gaps = 28/315 (8%)

Query: 1   MIRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTI 60
           MI+FD V+K Y D  T AV+ + L+   G+    +GPSGCGKTT+L+MINRLI  T+GTI
Sbjct: 1   MIKFDKVTKAYPDG-TIAVDALDLECPTGKITALVGPSGCGKTTSLRMINRLIEPTSGTI 59

Query: 61  YINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELL 120
            ++ +  +  D   LR  IGYV+Q   LFPH TI +NIA +P L   SK++   R  ELL
Sbjct: 60  SLDGESTAGMDPALLRRRIGYVIQHAGLFPHRTIVDNIATMPRLLGASKKESRTRAMELL 119

Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180
           ++VGL   ++  R P +LSGG+QQRVGV RALAADP  +LMDEPFSA+DP+ R +LQ + 
Sbjct: 120 ETVGLTT-NFADRYPWQLSGGQQQRVGVARALAADPSFMLMDEPFSAVDPVVRGQLQDEF 178

Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQ-GGEIVQVATPQEIMKNPENDFVKDFLA 239
             LQK+I KTI+ VTHD+ EAL LGD++ V++ GG + Q ATP E++  P ++FV DF+ 
Sbjct: 179 LRLQKEIGKTIIIVTHDIDEALKLGDQVVVLRTGGILAQAATPLELLTQPADEFVADFVG 238

Query: 240 SGHAFNTPILEANFTVNDLIEADLFYSYQTSDGTLGISSTEPVENL------VRRIAEEQ 293
               + +                    + T DG L   S EPV +L       R +  + 
Sbjct: 239 RDRGYRS------------------LGFTTLDGDLPTVS-EPVAHLGDSAAAARALTGDT 279

Query: 294 SIPVTDEAGNYIGTV 308
            + V D A   +G V
Sbjct: 280 WLLVVDPANKPLGWV 294


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: 308
Number of extensions: 11
Number of successful extensions: 4
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: 371
Length adjustment: 29
Effective length of query: 299
Effective length of database: 342
Effective search space:   102258
Effective search space used:   102258
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 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