Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate 3607949 Dshi_1357 ABC transporter related (RefSeq)
Query= TCDB::P54933 (332 letters) >FitnessBrowser__Dino:3607949 Length = 349 Score = 370 bits (950), Expect = e-107 Identities = 203/348 (58%), Positives = 240/348 (68%), Gaps = 16/348 (4%) Query: 1 MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60 MG ITL V+K FG+ VI +DL+I DGEFVVFVGPSGCGKSTLLR+I GLED S G + Sbjct: 1 MGAITLSKVEKWFGDVQVIKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRGAM 60 Query: 61 MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120 +IDG D T+ PPAKRGL MVFQSYALYPHM+V++N+ F L+ A EI +V AA + Sbjct: 61 LIDGVDVTDHPPAKRGLTMVFQSYALYPHMSVRENMGFSLKTAGAPAAEIAEKVEAAAAV 120 Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180 L L YLDRRP LSGGQRQRVAIGR+IVR P AFLFDEPLSNLDAALRV MR EI +LH Sbjct: 121 LKLEPYLDRRPKDLSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAKLH 180 Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240 QSL+TTMIYVTHDQVEAMT+AD+IVVL G+I QVG+P LY PANLFVA FIGSPKMN Sbjct: 181 QSLDTTMIYVTHDQVEAMTLADRIVVLEFGKIAQVGTPRELYETPANLFVAQFIGSPKMN 240 Query: 241 LIE---------------GPEAAKHGATTIGIRPEHIDLSRE-AGAWEGEVGVSEHLGSD 284 ++ G + A +GIRPEHI GA +G V V E+LG+D Sbjct: 241 VMPCTTDAGRYRLSAGRGGVFSGDRPAVQLGIRPEHITPGAPGTGACDGRVDVVEYLGAD 300 Query: 285 TFLHVHVAGMPTLTVRTGGEFGVHHGDRVWLTPQADKIHRFGADGKAL 332 T L + +TVR G+ + GD V L+ D++ F DG A+ Sbjct: 301 TLLVLDCGPEGRVTVRVIGDTDLTPGDAVGLSFNPDRLSFFDTDGLAI 348 Lambda K H 0.320 0.137 0.400 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: 367 Number of extensions: 13 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: 332 Length of database: 349 Length adjustment: 28 Effective length of query: 304 Effective length of database: 321 Effective search space: 97584 Effective search space used: 97584 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