Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate Ac3H11_794 Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_794 Length = 270 Score = 117 bits (293), Expect = 4e-31 Identities = 73/232 (31%), Positives = 118/232 (50%), Gaps = 7/232 (3%) Query: 146 PPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLA 205 P FT DNY + + ++NSL + VI + +A AAYA + F G + Sbjct: 46 PQHFTWDNYKTIFTDESWYSGYINSLIYVSINMVITLTVALPAAYAFSRYSFLGDKHVFF 105 Query: 206 VVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAG 265 ++ + P + L+P QLY VG T++ + LAH F +PLA+++L +M+G Sbjct: 106 WLLTNRMTPPAVFLLPFFQLYTTVGLM-----DTHIAVALAHLLFSVPLAVWILEGFMSG 160 Query: 266 LPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDK 325 +PREI E+A +DG S F+ I LPL + A F F+++W +LL+A Sbjct: 161 IPREIDETAYIDGYSFPRFFMTIFLPLIKAGVGVAAFFCFMFSWVELLLARTLTSVNAKP 220 Query: 326 LVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSV 377 +V T + + + G +W L A+ +TIV IV + ++ Y+ +G G V Sbjct: 221 IVAT--MTRTVSASGMDWATLAAAGVLTIVPGAIVIWFVRHYIAKGFAMGRV 270 Lambda K H 0.324 0.139 0.418 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: 254 Number of extensions: 17 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: 380 Length of database: 270 Length adjustment: 28 Effective length of query: 352 Effective length of database: 242 Effective search space: 85184 Effective search space used: 85184 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 (21.5 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