Align Galactofuranose-binding protein YtfQ (characterized)
to candidate BPHYT_RS23870 BPHYT_RS23870 LacI family transcription regulator
Query= SwissProt::P39325 (318 letters) >FitnessBrowser__BFirm:BPHYT_RS23870 Length = 328 Score = 271 bits (692), Expect = 2e-77 Identities = 151/321 (47%), Positives = 201/321 (62%), Gaps = 13/321 (4%) Query: 4 RLLIVSAVSAAMSSMALAAP--------LTVGFSQVGSESGWRAAETNVAKSEAEKRGIT 55 R L A+ A ++ LA P +T+GF+QVG+ES WR A T KS A I Sbjct: 10 RALGALALCAGFGALTLATPGAYAQDKQITLGFAQVGAESAWRTANTESIKSAAADAKIK 69 Query: 56 LKIADGQQKQENQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRSID 115 LK +D QQKQENQIKA+RS++AQ VD I +PVV +GWEPVL+EAK A+IPV L DR+ID Sbjct: 70 LKFSDAQQKQENQIKAIRSYIAQKVDVIAFSPVVESGWEPVLREAKAAKIPVILTDRNID 129 Query: 116 VKDKSLYMTTVTADNILEGKLIGDWLVKEVNGK--PCNVVELQGTVGASVAIDRKKGFAE 173 KD SLY+T + +D + EG+ G WL P N+ ELQGTVG++ A DR G E Sbjct: 130 TKDTSLYVTMIGSDFLEEGRRGGHWLEDHFKNDQGPINIAELQGTVGSAPANDRHSGLVE 189 Query: 174 AIKNAPNIKIIRSQSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIGAIQAIKE 233 IK+ P KII SQSGDFT + GK+VME+FIK N N+ VYAHNDDM +GAIQA++E Sbjct: 190 VIKSDPKFKIIASQSGDFTLAGGKQVMEAFIKTYGNKINV--VYAHNDDMALGAIQAMEE 247 Query: 234 AGLKPGKDILTGSIDGVPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKKDGTMPEKL 293 AG+ PGKDI S D ++AM G+ N VE +P + A++ ++P+++ Sbjct: 248 AGMHPGKDITVVSFDATKGGFQAMAAGKMNVDVECSPLLGPQLMSAVKDVVAGKSLPKRI 307 Query: 294 TLTKSTLYLPDTAKEELEKKK 314 LT+ T++ A + L +K Sbjct: 308 -LTEETVFPMSVAAQTLPTRK 327 Lambda K H 0.313 0.130 0.363 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: 253 Number of extensions: 9 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: 318 Length of database: 328 Length adjustment: 28 Effective length of query: 290 Effective length of database: 300 Effective search space: 87000 Effective search space used: 87000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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