Align sucrose permease scrT (characterized)
to candidate CCNA_01191 CCNA_01191 transporter, major facilitator superfamily
Query= reanno::ANA3:7022816 (406 letters) >FitnessBrowser__Caulo:CCNA_01191 Length = 411 Score = 457 bits (1176), Expect = e-133 Identities = 230/386 (59%), Positives = 288/386 (74%) Query: 16 IRVLTYLMFFMFAMTSDAVGVIIPQLISEFGLSLSQASAFHYMPMIFIAISGLFLGFLAD 75 IR+LTYLMF MFAMT+D+VGVIIP +I F L ++ A +FHY M IA+ G+ LGFLAD Sbjct: 15 IRILTYLMFMMFAMTTDSVGVIIPHVIKTFDLGMAAAGSFHYASMTGIALGGVCLGFLAD 74 Query: 76 KIGRKLTILLGLLLFAIACFLFALGESFYYFLLLLALVGLAIGVFKTGALALIGDISRST 135 ++GRK TI+LGL+ FA+ FLFA+G+ F +F+ LL L GLAIGVFKTGALALIGDIS ST Sbjct: 75 RLGRKATIVLGLVAFAVTAFLFAVGKDFGFFVALLFLSGLAIGVFKTGALALIGDISSST 134 Query: 136 KQHSSTMNTVEGFFGVGAMVGPAIVSYLLISGVSWKYLYFGAGVFCLLLCWLAFRADYPQ 195 + H++TMN VEGFFG+GA++GPAIV+ LL G SWK+LY AG C+LL A YPQ Sbjct: 135 RAHTATMNMVEGFFGLGAILGPAIVTALLAQGASWKWLYVIAGALCVLLIIAALNVRYPQ 194 Query: 196 VKRSSTETINLTNTFSMMKNPYALGFSLAIGLYVATEVAIYVWMPSLLQEYQGDYTVLAA 255 ++ + ++ T +M NPYAL FS AI LYV E AIYVWMP+LL +Y+G +LAA Sbjct: 195 TPPAAQQKLDPRVTLAMFGNPYALAFSFAIMLYVGVETAIYVWMPTLLADYKGPAVLLAA 254 Query: 256 YALTIFFTLRAGGRFLGGWILNHFSWQQVMFWFSLAISLCYLGSMLYGVEAAVILLPLSG 315 YAL++FF LRA GRFLG W+LN SW QV+ S+AI +C+ ++ G AV LP+SG Sbjct: 255 YALSVFFILRAAGRFLGAWLLNRLSWTQVVAICSVAILICFAAALAGGRAVAVYSLPISG 314 Query: 316 LFMSMMYPTLNSKGISCFPVAQHGSVAGVILFFTAVSAALAPLCMGLVGDIFGHVKYGFY 375 LFMS++YPT+NSKGISCFP A+HGSV+GVILFFT VSA +AP MGL+ D FG YGF Sbjct: 315 LFMSVLYPTINSKGISCFPKAEHGSVSGVILFFTCVSAVIAPWMMGLISDRFGDAVYGFA 374 Query: 376 LATGFAVLLCLLAGVNLIKDPSQALL 401 LATG A LL +LA +NL+ DPS+A L Sbjct: 375 LATGLAALLAVLAVLNLVFDPSRARL 400 Lambda K H 0.330 0.143 0.437 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: 532 Number of extensions: 17 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: 406 Length of database: 411 Length adjustment: 31 Effective length of query: 375 Effective length of database: 380 Effective search space: 142500 Effective search space used: 142500 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 (21.9 bits) S2: 50 (23.9 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