Align ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized)
to candidate SMa2307 SMa2307 ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1895 (302 letters) >FitnessBrowser__Smeli:SMa2307 Length = 307 Score = 119 bits (297), Expect = 1e-31 Identities = 87/286 (30%), Positives = 154/286 (53%), Gaps = 14/286 (4%) Query: 19 WL-PKLVLAPSMLIVLVGFYGYIIWTFILSFTNSSFMPSYKWVGLQQYMRLMDNDRWWVA 77 WL P L++ P ++ V + + +S + W+GL Y L+++ +++V+ Sbjct: 11 WLTPTLLILPGAILFAVVILASSVQSLWISLHDWDGFGPMIWIGLGNYRELINDPQFYVS 70 Query: 78 SKNLALFGGMFISISLVLGVFLAVLLDQRIRKEGFIRTVYLYPMALSMIVTGTAWKWLLN 137 KN ++ MF+ ++ +G+ +A+L++Q+I+ +R V P+ L+ + G + W+ Sbjct: 71 LKNNLIWLVMFM-LAPPIGLAIALLVNQKIKG---MRVVI--PLVLASVAVGVVFTWVYT 124 Query: 138 PGLGLDKML-RDWGWEGFRLDWLVDQDRVVYCLVIAAVWQASGFVMAMFLAGLRGVDQSI 196 P GL ++ R +G L L D+ V + +VIAA+W F M ++LAGL + + + Sbjct: 125 PEFGLLALIFRAFGANAPAL--LSDEHLVTFAIVIAALWPQIAFCMVLYLAGLNNLSEEL 182 Query: 197 IRAAQVDGASLPTIYLKIVLPSLRPVFFSAFMILAHIAIKSFDLVAAMTAGGPGYSSDLP 256 I A +VDGA + IVLP L V F A + A++SFD+++ MT GGP SS + Sbjct: 183 IGAGRVDGARGWNMLRHIVLPQLTQVTFIAIAVTVVGALRSFDMISVMTRGGPFGSSSVL 242 Query: 257 AMFMYSFTFSRGQMGIGS--ASAMLMLGAVLTILVPYLYSELRGKR 300 A M+ + + G G+ AS + ++ AVL LVP+ + RG++ Sbjct: 243 AYQMFEQSIFSYRFGYGAAIASVLFVIMAVL-YLVPHAHHP-RGRK 286 Lambda K H 0.329 0.141 0.448 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: 283 Number of extensions: 13 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: 302 Length of database: 307 Length adjustment: 27 Effective length of query: 275 Effective length of database: 280 Effective search space: 77000 Effective search space used: 77000 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 (21.8 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