GapMind for catabolism of small carbon sources

 

Aligments for a candidate for opuBA in Shewanella loihica PV-4

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 5208351 Shew_0863 ABC transporter-related protein (RefSeq)

Query= TCDB::Q93A35
         (328 letters)



>lcl|FitnessBrowser__PV4:5208351 Shew_0863 ABC transporter-related
           protein (RefSeq)
          Length = 342

 Score =  141 bits (356), Expect = 2e-38
 Identities = 83/222 (37%), Positives = 123/222 (55%), Gaps = 6/222 (2%)

Query: 19  VNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTIYINEKRISDYD--IHELR 76
           +  + L +  GE    +GPSGCGKTT LK I  L P++ G I IN + +S  +  +   R
Sbjct: 19  LRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISINGRLLSGPETFVPSER 78

Query: 77  WDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELLDSVGLDPESYRHRKPA 136
            ++G + Q  ALFPH+T+ ENI     +K   K     R+ E+L  V L  E    R P 
Sbjct: 79  REVGMIFQDYALFPHLTVAENILF--GVKGLDKAARQARLGEMLALVKL--EGLGGRYPH 134

Query: 137 ELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDISALQKKIKKTIVFVTH 196
           ELSGG+QQRV + RALA +P ++L+DEPFS +D   R  +  +I  + K+   + VFVTH
Sbjct: 135 ELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVEIREILKQRGVSAVFVTH 194

Query: 197 DMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFL 238
              EA    D++ + + G I Q  + + +   P + +V +FL
Sbjct: 195 SKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFL 236


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: 232
Number of extensions: 11
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: 342
Length adjustment: 28
Effective length of query: 300
Effective length of database: 314
Effective search space:    94200
Effective search space used:    94200
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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