Align LacG, component of Lactose porter (characterized)
to candidate BPHYT_RS17465 BPHYT_RS17465 glycerol-3-phosphate transporter membrane protein
Query= TCDB::P29824 (273 letters) >FitnessBrowser__BFirm:BPHYT_RS17465 Length = 281 Score = 142 bits (359), Expect = 6e-39 Identities = 86/277 (31%), Positives = 143/277 (51%), Gaps = 10/277 (3%) Query: 7 RRLPDIVQYSVLSLAAFLSIFPFIWMVIGTTNTTSQIIRGKVTF--GTALFDNIASFFAQ 64 RR D+ ++VL L L +FP T + ++ ++ T L +NIA+ ++Q Sbjct: 5 RRGFDLFCHAVLILGVVLVVFPVYVAFCAATMSEHEVFSVPLSLVPSTHLLENIATVWSQ 64 Query: 65 ------VDVPLVFWNSVKIALVGTALTLLVSSLAGYGFEMFRSKLRERVYTVILLTLMVP 118 + +NS+ +ALV + + VS ++ Y FR R + +I +TLM+P Sbjct: 65 GSGNAAAPFGRMLFNSLVMALVISIGKIAVSMISAYAIVFFRFPFRNLAFWLIFITLMLP 124 Query: 119 FAALMIPLFMLMGQAGLLNTHIAIMLPMIASAFIIFYFRQASKAFPTELRDAAKVDGLKE 178 + P ++ L NT+ + LP+IASA F FRQ P EL +AA++DG Sbjct: 125 VEVRIFPTVQVVSSMHLSNTYSGLTLPLIASATATFLFRQFFMTLPDELMEAARIDGAGA 184 Query: 179 WQIFFYIYVPVMRSTYAAAFVIVFMLNWNNYLWPLIVLQSNDTKTITLVVSSLASA--YS 236 + F+ + +P+ ++ AA FVI F+ WN YLWP+++ T + + S+ ++ + Sbjct: 185 MRFFWDVVLPLSKTNMAALFVITFIYGWNQYLWPILITSQQSLTTAVVGIKSMIASGDTA 244 Query: 237 PEYGTVMIGTILATLPTLLVFFAMQRQFVQGMLGSVK 273 E+ VM T+LA LP L V MQR FV+G++ + K Sbjct: 245 TEWHLVMTATLLAMLPPLAVVLTMQRWFVRGLVDAEK 281 Lambda K H 0.331 0.140 0.416 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: 255 Number of extensions: 17 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: 273 Length of database: 281 Length adjustment: 25 Effective length of query: 248 Effective length of database: 256 Effective search space: 63488 Effective search space used: 63488 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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