Align Sugar ABC transporter, periplasmic sugar-binding protein (characterized, see rationale)
to candidate BPHYT_RS27195 BPHYT_RS27195 LacI family transcriptional regulator
Query= uniprot:Q9WXW9 (335 letters) >FitnessBrowser__BFirm:BPHYT_RS27195 Length = 315 Score = 133 bits (335), Expect = 5e-36 Identities = 102/321 (31%), Positives = 156/321 (48%), Gaps = 28/321 (8%) Query: 13 MRKLLVFLSVLLVAGLSLALT------IGVIGKSVHP-YWSQVEQGVKAA-GKALGVDTK 64 M+KL V + + + A I VI K+ + YW V++G AA A G Sbjct: 1 MKKLSVLAAAAAMCAMFSAYAQAAGGEIAVIVKTANSNYWQNVQKGATAAMADAKGYTMT 60 Query: 65 FFVPQKEDINA-QLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSP 123 F P E A ++ M+E+ + V GI +APSDP A++P +KKA E IPVV +D+ Sbjct: 61 FQGPAAESAIADEVNMVENAVNRHVAGIVLAPSDPDALVPAMKKAWEAHIPVVLIDSTVS 120 Query: 124 DSGRYVY---IGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIK 180 D+G+ Y + TDN +AG M + +G GKV I + A + + R+ GF+ I Sbjct: 121 DAGKQYYQSFLSTDNTKAGELCAQAMIDRVGQTGKVAIMSYVPGAGSEIGRVGGFRKYIT 180 Query: 181 -DSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGK 239 S++++V + A A++ L+A+PDL FG + +GK GK Sbjct: 181 AHSKLQVVGPFYSQSQMATALNQTTDVLSANPDLKGIFGANEPTAVGMGRALAQSGKSGK 240 Query: 240 VKIVCFDTTPDILQYVKEGVIQATMGQRPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKV 299 V + FD D+ +V++G IQA Q Y MGY G+Q + ++ + V Sbjct: 241 VIAIGFDGNQDLQGFVRDGTIQAIAVQSSYQMGYK-----------GIQTLVNVIERKPV 289 Query: 300 DGKVDYVIDTGVDVVTPENLD 320 +V DTGV +V +NLD Sbjct: 290 SKQV----DTGVMMVEKQNLD 306 Lambda K H 0.318 0.137 0.388 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: 244 Number of extensions: 16 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: 335 Length of database: 315 Length adjustment: 28 Effective length of query: 307 Effective length of database: 287 Effective search space: 88109 Effective search space used: 88109 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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