Align Solute-binding protein Bamb_6123 (characterized)
to candidate BPHYT_RS24175 BPHYT_RS24175 C4-dicarboxylate ABC transporter
Query= SwissProt::Q0B2F6 (328 letters) >FitnessBrowser__BFirm:BPHYT_RS24175 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.
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:
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