Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate BWI76_RS07235 BWI76_RS07235 hypothetical protein
Query= uniprot:A0KWY4 (313 letters) >FitnessBrowser__Koxy:BWI76_RS07235 Length = 307 Score = 131 bits (330), Expect = 2e-35 Identities = 95/314 (30%), Positives = 161/314 (51%), Gaps = 10/314 (3%) Query: 1 MKHNKIITALGLWAVSATCAYATTVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADA 60 +K + + + + A +VG S + + T A++ E ++ G+ + DA Sbjct: 3 IKKTVVASLIACMLPAVVMAKDISVGVSMALFDDNFLTILRTAMQKEMQKDGVKAQVEDA 62 Query: 61 QQKQENQIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSL 120 + Q++ V++FI QGVDAII+ PV KP++ +A +A IP++ V+R + Sbjct: 63 KGDVSQQLQQVQNFIGQGVDAIIVNPVDTNAVKPIMDQATKAGIPLIFVNRRPQAQLTDK 122 Query: 121 FLTRIASDFSEEGRKIGQWLMDKTQGNCDIAELQGTVGATAAIDRAAGFNQVIANYPNAK 180 + + SD GR + L G ++A L G + + DR G +V+A YP+ K Sbjct: 123 -MAYVGSDSVLAGRLQMEALAKAMNGKGNVAILLGDLANESTRDRTKGVEEVVAKYPDIK 181 Query: 181 IVRSQTGEFTRAKGKEVMEGFLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDIL 240 IV+ QT +FTR +V+ ++ +G+ + A+ S+NDEMA+GA+QA+ G P IL Sbjct: 182 IVQKQTAKFTRNDAVDVVSNWM--TSGEDIQAIASNNDEMAIGALQAL---GKNP-NHIL 235 Query: 241 IVSVDGVPDYFKAMADGDVNATV-ELSPYLGGPAFDAIDAYLKGNKDQAKLISTTGDVFT 299 I VDG PD + + +G + AT+ + + G A DA G K + K+I + T Sbjct: 236 IAGVDGTPDALQMLKNGKMIATIFQDAKGQGEGAVDAAIKLANGEKVE-KVIDVPYQLIT 294 Query: 300 QETAAAEYEKRRQQ 313 ++ AE+ R Q+ Sbjct: 295 KDN-MAEFVNRNQK 307 Lambda K H 0.316 0.131 0.376 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: 249 Number of extensions: 15 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: 313 Length of database: 307 Length adjustment: 27 Effective length of query: 286 Effective length of database: 280 Effective search space: 80080 Effective search space used: 80080 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 (21.6 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