Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate HSERO_RS01335 HSERO_RS01335 sugar ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896 (281 letters) >FitnessBrowser__HerbieS:HSERO_RS01335 Length = 283 Score = 169 bits (427), Expect = 8e-47 Identities = 92/271 (33%), Positives = 157/271 (57%), Gaps = 7/271 (2%) Query: 16 AIY-ATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWP---TVIDGIGWIKAWDVVG 71 A+Y A+L +A ++L+P++ L+TS +S +++ GN WP +++ + Sbjct: 15 ALYRASLPVALLIWLLPMLAALVTSIRSNDELMAGNYWGWPQDFAMLENYREALTASPML 74 Query: 72 GYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASF 131 YFWNS IT+P+V+ + + AM G+ LS ++FRG+ + F + F+P Q +++P Sbjct: 75 HYFWNSCLITIPSVIGAISLAAMAGFALSTYQFRGNTVLFATFVACNFVPQQILMIPVRD 134 Query: 132 TLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLKIL 191 GL NT TG++L H+ F TLF RN+ +P +++AAR++GA +T+F +I+ Sbjct: 135 LSLSLGLFNTITGMMLFHIAMQTGFCTLFLRNFIKQLPFEMIEAARIEGASEWTVFYRIV 194 Query: 192 LPMSIPIVMVCLIWQFTQIWNDFLFGVVFASG-DAQPITVALNNLVNTSTGAKEYNVDMA 250 LP+ P + + FT +WND+ + +V G D PITV + L T A +N+ A Sbjct: 195 LPLIRPALAALAVLVFTFVWNDYFWALVLTQGDDVAPITVGVAALRGQWTTA--WNLVSA 252 Query: 251 AAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 +++A LP+++++ K F+ GLT GA KG Sbjct: 253 GSILAALPSVILFFVMQKQFVAGLTFGASKG 283 Lambda K H 0.329 0.143 0.447 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: 228 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 281 Length of database: 283 Length adjustment: 26 Effective length of query: 255 Effective length of database: 257 Effective search space: 65535 Effective search space used: 65535 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: 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