GapMind for catabolism of small carbon sources

 

Aligments for a candidate for opuBA in Bacteroides thetaiotaomicron VPI-5482

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 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

Query= TCDB::Q93A35
         (328 letters)



>lcl|FitnessBrowser__Btheta:350819 BT1291 spermidine/putrescine
           transport ATP-binding protein (NCBI ptt file)
          Length = 463

 Score =  179 bits (454), Expect = 1e-49
 Identities = 98/245 (40%), Positives = 145/245 (59%), Gaps = 6/245 (2%)

Query: 1   MIRFDNVSKKYSDDKTAAVNNVTLDIKDGEFFVFIGPSGCGKTTTLKMINRLIPLTTGTI 60
           +I   +VSK + D    A+++VTL++K GEF   +GPSGCGKTT L++I      + G I
Sbjct: 9   IIEVSHVSKFFGDK--TALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEI 66

Query: 61  YINEKRISDYDIHELRWDIGYVLQQIALFPHMTIEENIAIVPELKKWSKEKIHDRITELL 120
            I+ K I+    H+    +  V Q+ ALFPH+ + +NIA   +LKK  K+ I  ++   L
Sbjct: 67  RISGKEITQTPPHKR--PVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAAL 124

Query: 121 DSVGLDPESYRHRKPAELSGGEQQRVGVVRALAADPGIILMDEPFSALDPISRQRLQQDI 180
             VG+    Y +R    LSGG+QQRV + RA+  +P ++L+DEP +ALD   R+ +Q ++
Sbjct: 125 KMVGMT--DYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMEL 182

Query: 181 SALQKKIKKTIVFVTHDMQEALALGDRICVMQGGEIVQVATPQEIMKNPENDFVKDFLAS 240
             + K +  T V+VTHD +EAL L D I VM  G+I Q+ TP +I   P N FV DF+  
Sbjct: 183 KEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE 242

Query: 241 GHAFN 245
            +  N
Sbjct: 243 SNILN 247


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: 387
Number of extensions: 12
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: 463
Length adjustment: 30
Effective length of query: 298
Effective length of database: 433
Effective search space:   129034
Effective search space used:   129034
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: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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