Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate BPHYT_RS22030 BPHYT_RS22030 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__BFirm:BPHYT_RS22030 Length = 341 Score = 186 bits (472), Expect = 7e-52 Identities = 113/330 (34%), Positives = 184/330 (55%), Gaps = 22/330 (6%) Query: 5 LLKAENVRAYYKLE--------KVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIF 56 LL+ +N++ + + K +++AVDG+SF + E +G+VGESGCGK+TL+ I Sbjct: 14 LLRVDNLKVQFGVPRGGFPWSGKATLRAVDGVSFNVRRGETVGLVGESGCGKSTLARAI- 72 Query: 57 MNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRME 116 + + G + R G+ L R+ + + +++ +I Q + +L P + +E Sbjct: 73 ---IGLAPVASGSV--RWLGDETVLPGARRNTSRLR---RDVQMIFQDPLASLDPRMTIE 124 Query: 117 KYVRHLAESHGID--EEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATIL 174 + V +HG D ++ + E VGL+ ++RYP E SGG QR IA A I Sbjct: 125 QIVSEPLTTHGQDVARADVQRRVLTMLERVGLNAQHLRRYPHEFSGGQCQRVGIARALIG 184 Query: 175 NPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYA 234 P L+I DEP SALDV Q ++ +L ++R+ + S++F+ HD+A V+ I+ R+++MY Sbjct: 185 EPQLVICDEPVSALDVSIQAQIVNLLRDLQRE-LSLSLLFVAHDLAVVKAISHRVLVMYL 243 Query: 235 GKIVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKK-RGITTIPGAPPNLINPPSGCRF 293 G+++EF + P HPYT+ L ++V P+P V++ R + G + +NPPSGC F Sbjct: 244 GRVMEFGDKREVYGTPRHPYTRALLSAVPVPDPVVERARRHLLLRGEIASPLNPPSGCAF 303 Query: 294 HPRCPHAMDVCKEKEP-PLTEIEPGRRVAC 322 RCP A+D C + P P+T RVAC Sbjct: 304 RTRCPDAIDACAREIPQPVTHGARATRVAC 333 Lambda K H 0.321 0.138 0.405 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: 281 Number of extensions: 10 Number of successful extensions: 4 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: 330 Length of database: 341 Length adjustment: 28 Effective length of query: 302 Effective length of database: 313 Effective search space: 94526 Effective search space used: 94526 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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