GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacI in Paraburkholderia bryophila 376MFSha3.1

Align Xylose/arabinose import permease protein XacI (characterized, see rationale)
to candidate H281DRAFT_00168 H281DRAFT_00168 carbohydrate ABC transporter membrane protein 2, CUT1 family

Query= uniprot:D4GP37
         (309 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00168 H281DRAFT_00168
           carbohydrate ABC transporter membrane protein 2, CUT1
           family
          Length = 285

 Score =  153 bits (387), Expect = 4e-42
 Identities = 93/299 (31%), Positives = 153/299 (51%), Gaps = 29/299 (9%)

Query: 19  VNLRRVAQYALVVFFLGFFLVPLETGIMTAIKTNESVARSLPFAPPVG-------EGFTL 71
           + + R   YA +V F  +FL PL   + T+ K  + +       PP         + ++ 
Sbjct: 5   MTISRAVIYAALVLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPPSHWTVEPWIKAWSG 64

Query: 72  GNIQFALEQLSGSFFNSLIMSIPATIGSVLFGSMAAYGLTMVNWRAQMGMLMLFVVGVFV 131
                  + +   F NS+ M IPA + S + G+   Y LT   +R    +  + +VG F+
Sbjct: 65  ACTGVRCDGMQPFFMNSVRMVIPAVLLSSIIGAFNGYVLTHWRFRGADPIFTMLLVGCFI 124

Query: 132 PYQAVLVPLARFWNNIFPLARMIEPMVASIPFFQGYHAELVPLVITHIAYGIPICTILFR 191
           P+QA+L+P+ARF                    F G       LV+ H+ YGI   T+ FR
Sbjct: 125 PFQAILLPMARFEG------------------FLGLSNTTTGLVVVHVIYGIAFTTMFFR 166

Query: 192 SYYQSLPNSLVEAGKIDGASITKIYRRIILPISKPMFGVVFIYQFTQIYNEFLFAFTLVT 251
           ++Y S+P  LV+A +IDGA    I+ +I+LP+S P+F V  I+QFTQI+N+FLF    + 
Sbjct: 167 NFYVSIPAELVKAARIDGAGFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFG---IV 223

Query: 252 GSDAPAAPVTLVLPAIGASTSGI-NFGIRMSAAFLAAVPTLILYVAFAEQFAKGLRTEA 309
            S   + P+T+ L  +  +++G+  + + M+ A +AA+PTL++Y+     F +GL   A
Sbjct: 224 FSGVDSMPITVALNNLVNTSTGVKEYNVDMAGAIIAALPTLLVYIVAGRYFVRGLTAGA 282


Lambda     K      H
   0.328    0.141    0.413 

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: 256
Number of extensions: 14
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: 309
Length of database: 285
Length adjustment: 26
Effective length of query: 283
Effective length of database: 259
Effective search space:    73297
Effective search space used:    73297
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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 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