Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate SMc02031 SMc02031 permease
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__Smeli:SMc02031 Length = 349 Score = 256 bits (654), Expect = 6e-73 Identities = 143/313 (45%), Positives = 205/313 (65%), Gaps = 12/313 (3%) Query: 25 LLGLIVLFSFLS---NRFLTLENFWIILRQTAVNLCIAVGMTFVILTGGIDLSVGSILGF 81 L+ L++L ++L+ + FLTL+N + RQ+A +AVG TFVILTGGIDLSV +I Sbjct: 33 LIALVLLMAYLAFATSNFLTLDNLSNVARQSAFVAILAVGQTFVILTGGIDLSVAAIAAL 92 Query: 82 SGAVTAKLLKYGLILSAFGVVLKFNPLGASI-IGVLAGFAIGLFNGFIITRFNIPPFVAT 140 S ++TA LL L+L FG+ F P +I IG+L G A G NG++I++F IP F+AT Sbjct: 93 SASITAVLLTQPLVL--FGIDFGFVPPPVAILIGILIGMAAGALNGWLISKFKIPDFIAT 150 Query: 141 LGTMTAVRGFIMLLTKGHPIT------RLGDSFDFIGSGWFLGIPMPVWIAAIATGVGIF 194 LGTMTA RG +L+T G P+ +L +S ++G G G+P+ IA + G + Sbjct: 151 LGTMTAFRGAALLVTDGLPVPSFNAGRQLPESLIWVGGGQLFGVPVSALIALLCAAAGWY 210 Query: 195 ILRKTQFGRYVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAVAGLIVTARLDSAQPN 254 +LR T GR +YAVGGN AA SG++ TK+ YAISG+L+A+AG+I+ RL+SA Sbjct: 211 VLRYTALGRAIYAVGGNRAAAHSSGISISRTKIMTYAISGLLAAIAGIILVGRLNSANAL 270 Query: 255 AGLMYELDAIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLVLVGVSPFWQQVAKGF 314 EL +IA+ VIGG +L GG+G + G+++GA IIGVL +GL L+ VSPFWQ++A+G Sbjct: 271 MADGEELRSIASVVIGGTNLFGGEGGVWGSIIGAAIIGVLGNGLNLLDVSPFWQRIAQGV 330 Query: 315 IIIAAVIAEKLGR 327 +I+ VI ++ R Sbjct: 331 VIVVVVIFDQWRR 343 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: 389 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 331 Length of database: 349 Length adjustment: 28 Effective length of query: 303 Effective length of database: 321 Effective search space: 97263 Effective search space used: 97263 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