Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate GFF1302 PGA1_c13180 ABC transporter, ATP binding protein
Query= TCDB::P54933 (332 letters) >FitnessBrowser__Phaeo:GFF1302 Length = 334 Score = 481 bits (1238), Expect = e-140 Identities = 243/330 (73%), Positives = 272/330 (82%), Gaps = 1/330 (0%) Query: 1 MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60 MG+I L +V K FG VIP LDL IEDGEF VFVGPSGCGKSTLLRLIAGLED++ G I Sbjct: 1 MGQIKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTI 60 Query: 61 MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120 IDG DAT +PPAKRGLAMVFQSYALYPHM+V+KNIAFP++MA + E +RR+ NAA Sbjct: 61 RIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAA 120 Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180 LNLT+YLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRV MRLEI+ELH Sbjct: 121 LNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELH 180 Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240 + L TTMIYVTHDQVEAMTMADKIVVL AG IEQVGSP+ LYR P N+FVAGFIGSPKMN Sbjct: 181 KRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMN 240 Query: 241 LIEGPEAAKHGATTIGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHV-AGMPTLTV 299 L+ GP+AA+H A TIGIRPEH+ +S G W G +GVSEHLGSDTF HV A LTV Sbjct: 241 LLTGPQAAQHNAATIGIRPEHLSISETEGMWAGTIGVSEHLGSDTFFHVQCDAFDDPLTV 300 Query: 300 RTGGEFGVHHGDRVWLTPQADKIHRFGADG 329 R GE + +G+RV+LTP +HRFG+DG Sbjct: 301 RASGELDLGYGERVFLTPDMTHLHRFGSDG 330 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: 429 Number of extensions: 10 Number of successful extensions: 2 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: 334 Length adjustment: 28 Effective length of query: 304 Effective length of database: 306 Effective search space: 93024 Effective search space used: 93024 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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