GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Caulobacter crescentus NA1000

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 CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA

Query= TCDB::Q93A35
         (328 letters)



>FitnessBrowser__Caulo:CCNA_03235
          Length = 381

 Score =  180 bits (457), Expect = 4e-50
 Identities = 100/244 (40%), Positives = 150/244 (61%), Gaps = 6/244 (2%)

Query: 1   MIRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTI 60
           +I F+NV+K++   K AAV+NV+L + +GEFF  +GPSGCGKTT L+M+      T G I
Sbjct: 14  IITFENVTKRFG--KLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRI 71

Query: 61  YINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELL 120
            I+ + IS+  +   +  +  V Q  A+FPHMT+ +N+A   ++    K +   R+ E L
Sbjct: 72  LIDGQDISN--VPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEAL 129

Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180
           + V L       RKP +LSGG++QRV + RAL   P ++L+DEP SALD   R++++ ++
Sbjct: 130 ELVQLG--GLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTEL 187

Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240
             LQ+K+  T + VTHD  EALAL  R  VM  G + QVATP ++ + P + FV DF+  
Sbjct: 188 CTLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQ 247

Query: 241 GHAF 244
            + F
Sbjct: 248 VNLF 251


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: 286
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: 381
Length adjustment: 29
Effective length of query: 299
Effective length of database: 352
Effective search space:   105248
Effective search space used:   105248
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 17 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