Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 236 bits (601), Expect = 8e-67 Identities = 134/326 (41%), Positives = 188/326 (57%), Gaps = 27/326 (8%) Query: 16 ISRYQSIFILLGLIVLFSFLSNRFLTLENFWIILRQTAVNLCIAVGMTFVILTGGIDLSV 75 I ++ ++ L+ LIV FS S F ++ N + Q + V T VI+TGGIDLSV Sbjct: 24 IQKFAALGSLVVLIVAFSLTSAAFFSVGNLMTVALQVTSIAYLGVAATCVIITGGIDLSV 83 Query: 76 GSILGFSGAVTAKLLKYGLILSAFGVVLKFNPLGASIIGVLAGFAIGLFNGFIITRFNIP 135 GS+L +G A L+K G+ + A + G+L G A G NG +TR +P Sbjct: 84 GSVLALAGVAAALLVKAGVPIPV-----------AMLGGMLVGAACGWVNGICVTRMGLP 132 Query: 136 PFVATLGTMTAVRGFIMLLTKGHPITRLGDSFDFIGSGW----------------FLGIP 179 PF+ATLG M RG + +T P++ LGD+F +G+G F GIP Sbjct: 133 PFIATLGMMLVARGLALQITGARPVSGLGDAFGELGNGALFRISHIGADGFPDTVFPGIP 192 Query: 180 MPVWIAAIATGVGIFILRKTQFGRYVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAV 239 PV I + +L +T GR++YAVG N +AA LSGVN + KL+ Y +SG+L+ Sbjct: 193 YPVVIMVVLFAAVSILLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKLFTYVLSGLLAGA 252 Query: 240 AGLIVTARLDSAQPNAGLMYELDAIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLV 299 G ++ +RL +AQPN G+MYELDAIA+ VIGG SL GG GT+ GT +GA +IGVL +GL Sbjct: 253 TGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGTAIGAFVIGVLRNGLN 312 Query: 300 LVGVSPFWQQVAKGFIIIAAVIAEKL 325 + GVS F QQ+ G +I+ V ++L Sbjct: 313 MNGVSSFIQQIIIGVVILGTVWIDQL 338 Lambda K H 0.327 0.144 0.427 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: 391 Number of extensions: 20 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: 331 Length of database: 343 Length adjustment: 28 Effective length of query: 303 Effective length of database: 315 Effective search space: 95445 Effective search space used: 95445 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: 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