Align Glucose/galactose transporter (characterized, see rationale)
to candidate CCNA_01159 CCNA_01159 transporter, major facilitator superfamily
Query= uniprot:A0KXM0 (423 letters) >FitnessBrowser__Caulo:CCNA_01159 Length = 451 Score = 255 bits (652), Expect = 2e-72 Identities = 160/432 (37%), Positives = 239/432 (55%), Gaps = 31/432 (7%) Query: 17 AGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYFLVS 76 A G + A+V +T LFF+W +T L D L+ +K VF+L +A L F FF AY ++S Sbjct: 11 AKGGGVKLAIVYVTCLFFIWALVTNLLDPLLKTMKTVFTLTPVEASLTGFAFFIAYGIMS 70 Query: 77 IPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQVAA 136 +P+ + +LGY + ++ GL GC + AA T+G+FL LFV ASG+T+LQVAA Sbjct: 71 LPSAAFLSKLGYARSVMVGLGGIVAGCFIAIAAAKLHTFGVFLVGLFVTASGVTLLQVAA 130 Query: 137 NPYVNALGSSETASSRLNLTQAFNALGTTVAPFFG-SILILSVAASVSSELAQANAEAEV 195 NP + ++G E +S RLNL+QAFN+LG +FG + L+ + + A E + Sbjct: 131 NPLIASMGKPEESSFRLNLSQAFNSLGAACGLWFGANFLLKGEIFEKDAVITDAMREQAL 190 Query: 196 --VKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSALQSMHLVLGAV 253 V YL + LA+ ++ + ++R+ AA + + +AL S LGA+ Sbjct: 191 GFVSNVYLAIGLGLALFILL-----IFMVRQKITEAAPKTGQLVNPFTALTSKWANLGAI 245 Query: 254 GIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFIGSAVMQKIPA 313 GIF+YVGAEV+I L+ FL ++HI+ + EQA +Y AM+GRF GSA+++ I Sbjct: 246 GIFLYVGAEVAISLHLLLFLEQSHILDISAEQAGKLTTFYMVFAMIGRFAGSALLKTIKD 305 Query: 314 GTVLAFNAFMAALLVLV----------------------AMTTSGSVAMWAILGVGLFNS 351 +LA A A L LV A T+G + +A L +GLFNS Sbjct: 306 YVMLAIVAVGAIALCLVVILTKDMTPSAHAGTVNLLLASAPVTTGLIPAFAALLIGLFNS 365 Query: 352 IMFPTIFSLALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLG-IQLAFILPVVCY 410 IMFPTIF+L L+ TS SG+LC+AIVGGA +PL + + G + + F P++CY Sbjct: 366 IMFPTIFTLTLQRSSAPTSATSGLLCMAIVGGAFLPLAFAKIEEMTGSMAMGFAAPLLCY 425 Query: 411 GFILFYGAKGSK 422 ++L++ K Sbjct: 426 VYVLWFALVAKK 437 Lambda K H 0.326 0.138 0.402 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: 509 Number of extensions: 22 Number of successful extensions: 3 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: 423 Length of database: 451 Length adjustment: 32 Effective length of query: 391 Effective length of database: 419 Effective search space: 163829 Effective search space used: 163829 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: 51 (24.3 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