Align TreT, component of Trehalose porter (characterized)
to candidate BPHYT_RS17460 BPHYT_RS17460 glycerol-3-phosphate transporter permease
Query= TCDB::Q97ZC2 (275 letters) >FitnessBrowser__BFirm:BPHYT_RS17460 Length = 294 Score = 101 bits (251), Expect = 2e-26 Identities = 87/275 (31%), Positives = 135/275 (49%), Gaps = 18/275 (6%) Query: 9 FLLVLPALAYVISFAFFPTIEAVYLSFQ--DPHGGFS----LYNYKEL--SYFNLSS--- 57 +LLV P LA + F +P EA++ S Q D G S L N+K+L LSS Sbjct: 14 YLLVAPQLAITLLFFLWPAGEALWQSTQSQDAFGTSSEFVGLANFKQLFADPLYLSSFYT 73 Query: 58 AIINTIVVTIGALAIQLALGFLVASVLSREFFGKRALSTITIIPMGIATVVAAVTFSFVF 117 +I +VT+ L I L L+A R G + T+ I P +A +AAV +SF+F Sbjct: 74 TLIFCALVTVSGLVISL----LLAVCADRVTRGAKTYQTLLIWPYAVAPAIAAVLWSFLF 129 Query: 118 QTSGGYANTILHSLFGLNVNWYQSSISSLLVVMIADSWKNTPIVALILLAGMSSIPKELY 177 S G L + +G+ N ++ ++ +V++A WK L AG+ +IP+ L Sbjct: 130 NPSIGLVTYAL-AKYGIVWNHALNAGQAMFLVVLASVWKQVSYNFLFFYAGLQAIPRSLI 188 Query: 178 YASAIDGAGPIRRFFYITLPNLRSFIGISLILRGVQE-FNIFALPLILIGEHPPLLT-TL 235 A+AIDGAGP+RRFF I LP L L++ F+ F + G P T TL Sbjct: 189 EAAAIDGAGPVRRFFGIALPLLSPTSFFLLVINITYAFFDTFPVIDAATGGGPAQATRTL 248 Query: 236 IYDLYTTTFPEVGLALASATILLGFILVFSGIVIK 270 IY ++ F + + + A ++ ++V + V++ Sbjct: 249 IYKIFAEGFQGLDIGSSGAQSVILMVIVVALTVVQ 283 Lambda K H 0.328 0.143 0.414 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: 198 Number of extensions: 12 Number of successful extensions: 1 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: 275 Length of database: 294 Length adjustment: 26 Effective length of query: 249 Effective length of database: 268 Effective search space: 66732 Effective search space used: 66732 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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