GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctP in Burkholderia phytofirmans PsJN

Align Solute-binding protein Bamb_6123 (characterized)
to candidate BPHYT_RS24175 BPHYT_RS24175 C4-dicarboxylate ABC transporter

Query= SwissProt::Q0B2F6
         (328 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS24175 BPHYT_RS24175
           C4-dicarboxylate ABC transporter
          Length = 330

 Score =  546 bits (1406), Expect = e-160
 Identities = 267/330 (80%), Positives = 297/330 (90%), Gaps = 2/330 (0%)

Query: 1   MTHRFPRSRTALAVA--LMAGFAMSAQARVFRSADVHGDSFPTNMAVKFMGDELSKLTGG 58
           M  +F  SR +L VA  ++A   +SAQARVFR +DVHGD++PTNMAVK MG+E++K TGG
Sbjct: 1   MNKKFAPSRVSLIVAASVLALSTVSAQARVFRVSDVHGDTYPTNMAVKHMGEEINKATGG 60

Query: 59  KDSIKVFGNSALGSEKDTVDQVRIGAIDMARVNGASFNEIVPESLIPSFPFLFRDVDHFR 118
           KDS+KVFGNSALGSE DT+DQVRIGA+DMAR NGA+FNEIVPES+IPS PFLFRD+DHFR
Sbjct: 61  KDSVKVFGNSALGSENDTIDQVRIGALDMARANGAAFNEIVPESMIPSLPFLFRDIDHFR 120

Query: 119 KAMYGPAGQKILDAFAAKGMIALTFYESGARSIYAKRPVRTPADMKGLKVRVQPSDLMVD 178
           K MYGP GQKILDAF AKGMIALTFYESGARSIY K+P+ TPADMKGLKVRVQPSDLMVD
Sbjct: 121 KVMYGPEGQKILDAFKAKGMIALTFYESGARSIYTKKPIHTPADMKGLKVRVQPSDLMVD 180

Query: 179 EIRAMGGTPTPMPFAEVYTGLKTGLVDAAENNLPSYEETKHFEVAPDYSETQHAMTPEVL 238
           EIRAMGGTPTPMPFAEVYTGLKTGLVDAAENNLPSYEETKHFEVAP YSETQH+MTPEVL
Sbjct: 181 EIRAMGGTPTPMPFAEVYTGLKTGLVDAAENNLPSYEETKHFEVAPVYSETQHSMTPEVL 240

Query: 239 VFSKKIWDTLSPQEQAAIRKAAADSVPYYQKLWTAREASAQQAVTKGGANILPAAQVDRA 298
           VFSKK+WDTL+PQEQ  I+KAAADSVPYYQKLWTAREA A + VTKGGA I+ + Q+DRA
Sbjct: 241 VFSKKVWDTLTPQEQEIIKKAAADSVPYYQKLWTAREADASKTVTKGGATIVASTQIDRA 300

Query: 299 AFVKAMQPLWTKYEKTPQMKQIVDEIEATK 328
           AFVKAMQP+W KYEKTPQMKQ+VDEI+A K
Sbjct: 301 AFVKAMQPVWAKYEKTPQMKQLVDEIQAVK 330


Lambda     K      H
   0.318    0.131    0.375 

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: 483
Number of extensions: 11
Number of successful extensions: 1
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: 330
Length adjustment: 28
Effective length of query: 300
Effective length of database: 302
Effective search space:    90600
Effective search space used:    90600
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