Align The Na+-dependent sugar transporter, HP1174 (transports glucose, galactose, mannose and 2-deoxyglucose (Psakis et al. 2009)). (most similar to 2.A.1.7.2; 49% identity) (characterized)
to candidate CCNA_01159 CCNA_01159 transporter, major facilitator superfamily
Query= TCDB::O25788 (407 letters) >FitnessBrowser__Caulo:CCNA_01159 Length = 451 Score = 211 bits (536), Expect = 5e-59 Identities = 147/426 (34%), Positives = 214/426 (50%), Gaps = 37/426 (8%) Query: 8 LALGSLTALFFLMGFITVLNDILIPHLKPIFDLTYFEASLIQFCFFGAYFIMGGVFGNVI 67 LA+ +T LFF+ +T L D L+ +K +F LT EASL F FF AY IM + Sbjct: 18 LAIVYVTCLFFIWALVTNLLDPLLKTMKTVFTLTPVEASLTGFAFFIAYGIMSLPSAAFL 77 Query: 68 SKIGYPFGVVLGFVITATGCALFYPAAHFGSYGFFLGALFILASGIVCLQTAGNPFVTLL 127 SK+GY V++G GC + AA ++G FL LF+ ASG+ LQ A NP + + Sbjct: 78 SKLGYARSVMVGLGGIVAGCFIAIAAAKLHTFGVFLVGLFVTASGVTLLQVAANPLIASM 137 Query: 128 SKGKEAR-NLVLVQAFNSLGTTLGPIFGSLLIFSTTKMGDNASLIDKLAD-----AKSVQ 181 K +E+ L L QAFNSLG G FG+ + +A + D + + +V Sbjct: 138 GKPEESSFRLNLSQAFNSLGAACGLWFGANFLLKGEIFEKDAVITDAMREQALGFVSNVY 197 Query: 182 MPY-LGLAVFSLLLALIMYLLKLPDVEKEMPKETTQKSLFSHKHFVFGALGIFFYVGGEV 240 + LGLA+F LL+ ++ K+ + + + + + K GA+GIF YVG EV Sbjct: 198 LAIGLGLALFILLIFMVRQ--KITEAAPKTGQLVNPFTALTSKWANLGAIGIFLYVGAEV 255 Query: 241 AIGSFLVLSFEK--LLNLDSQSSAHYLVYYWGGAMVGRFLGSVLMNKIAPNKYLAFNALS 298 AI L+L E+ +L++ ++ + +Y AM+GRF GS L+ I LA A+ Sbjct: 256 AISLHLLLFLEQSHILDISAEQAGKLTTFYMVFAMIGRFAGSALLKTIKDYVMLAIVAVG 315 Query: 299 SI----------------------VLIALAIIIGGKIALFALTFVGFFNSIMFPTIFSLA 336 +I +L+A A + G I FA +G FNSIMFPTIF+L Sbjct: 316 AIALCLVVILTKDMTPSAHAGTVNLLLASAPVTTGLIPAFAALLIGLFNSIMFPTIFTLT 375 Query: 337 TLNLGHLTSKASGVISMAIVGGALIPPIQGAVTDMLTATESNLLYAYGVPLLCYFYILFF 396 TS SG++ MAIVGGA +P + +M ++ + PLLCY Y+L+F Sbjct: 376 LQRSSAPTSATSGLLCMAIVGGAFLPLAFAKIEEM----TGSMAMGFAAPLLCYVYVLWF 431 Query: 397 ALKGYK 402 AL K Sbjct: 432 ALVAKK 437 Lambda K H 0.328 0.144 0.423 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: 445 Number of extensions: 22 Number of successful extensions: 6 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: 407 Length of database: 451 Length adjustment: 32 Effective length of query: 375 Effective length of database: 419 Effective search space: 157125 Effective search space used: 157125 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