Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate AZOBR_RS27940 AZOBR_RS27940 ABC transporter permease
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__azobra:AZOBR_RS27940 Length = 329 Score = 134 bits (338), Expect = 2e-36 Identities = 93/311 (29%), Positives = 166/311 (53%), Gaps = 21/311 (6%) Query: 26 VALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGIDLS 85 +AL ++++ ++V P F L G + ++L R A + ++A+G T VI GGIDLS Sbjct: 21 LALAALIVLGTIVNPVF----LSPGNIG----NVLTRTAFIGIIAVGATFVITAGGIDLS 72 Query: 86 VGAVMAIAGATTAAMTVA-----GFSLPIVLLS---ALGTGILAGLWNGILVAILKIQPF 137 VG++ A A + A G LP++L+ ALG G++AGL NG+LV +++ F Sbjct: 73 VGSLAAFASGVMIVVMNALVGSMGAGLPVILIGVLVALGLGLVAGLVNGLLVTKGRMEAF 132 Query: 138 VATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGS---GSLLFLPTPVIIAVLTLILFWL 194 + TL M R + I G ++ NS + + G + + P++ + ++ L Sbjct: 133 IVTLGTMGIFRSLVTYIADGGTLSLNSEIRTIYRPVYYGGVFGISYPILAFAVVALIGAL 192 Query: 195 LTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADAN 254 + +T G + A+G + A+ + +N + +L +VL G+C AIA +I + A A Sbjct: 193 IMYRTRFGRYCAAIGSSEDVARYSAINVDRVKLLAFVLQGICVAIAVVIYVPRLGSASAT 252 Query: 255 NAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSG-FPPEMNQVVK 313 LW EL+AI AV+IGG L GG + +VVGA+++ ++ + L+G +N ++ Sbjct: 253 TGLLW-ELEAIAAVIIGGTMLKGGYGRIWGTVVGAVMLTLIDNILNLTGAISVYLNGTIQ 311 Query: 314 AVVVLCVLIVQ 324 V+++ +++Q Sbjct: 312 GVIIIVAVLLQ 322 Lambda K H 0.327 0.142 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: 283 Number of extensions: 19 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: 341 Length of database: 329 Length adjustment: 28 Effective length of query: 313 Effective length of database: 301 Effective search space: 94213 Effective search space used: 94213 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: 49 (23.5 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