Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate BPHYT_RS14815 BPHYT_RS14815 methionine ABC transporter permease
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__BFirm:BPHYT_RS14815 Length = 217 Score = 75.9 bits (185), Expect = 9e-19 Identities = 61/197 (30%), Positives = 104/197 (52%), Gaps = 21/197 (10%) Query: 148 TLALVLTALLFCIVIGLPLGIWLARSPRAA--------KIIRPLLDAMQTTPAFVYLVPI 199 TL +V + L ++GLPLG+ L + R + + +++A+++TP + LV + Sbjct: 16 TLVMVGISGLVGALVGLPLGVVLYLTDRQGVLQNIAVNRAMGVIVNAVRSTPFIILLVAV 75 Query: 200 V----MLFG--IGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFGASPRQMLF 253 + ++ G IG VV I A P I RL + +V LIEA+++ GA+ Q++F Sbjct: 76 IPFTRLVVGSSIGTAAAVVPLTIAAAPFIARLVETALREVDRGLIEAAQAMGATTSQIVF 135 Query: 254 KVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLR-GIGR-LDMGLATVGGV 311 KV LP ++P ++AG+ T + + +A I GGLG + +R G R L + TV Sbjct: 136 KVLLPESLPGVVAGLTITFVSLVGYSAMAGAIGGGGLGDLGIRYGYQRFLPEVMLTV--- 192 Query: 312 GIVILAIILDRLTQAVG 328 V++ I+ +L Q+ G Sbjct: 193 --VVILIVFVQLVQSFG 207 Lambda K H 0.326 0.141 0.435 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: 188 Number of extensions: 9 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: 354 Length of database: 217 Length adjustment: 25 Effective length of query: 329 Effective length of database: 192 Effective search space: 63168 Effective search space used: 63168 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 47 (22.7 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