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 7025962 Shewana3_3110 glucose/galactose transporter (RefSeq)
Query= TCDB::O25788 (407 letters) >FitnessBrowser__ANA3:7025962 Length = 432 Score = 180 bits (456), Expect = 8e-50 Identities = 146/432 (33%), Positives = 215/432 (49%), Gaps = 41/432 (9%) Query: 2 QKTSNTLALGSLTALFFLMGFITVLNDILIPHLKPIFDLTYFEASLIQFCFFGAYFIMGG 61 Q+ S+ L + + ALFF++GF T LN L+P+LK I L F+ASLI F F+ A Sbjct: 7 QQKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTAL 66 Query: 62 VFGNVISKIGYPFGVVLGFVITATGCALFYPAAHFGSYGFFLGALFILASGIVCLQTAGN 121 VI K+GY G+ LG I LF PAA +G FL A ++ +G LQTA N Sbjct: 67 PSAWVIRKVGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQTAVN 126 Query: 122 PFVTLLSKGKEARNLVLVQAFNSLGT-TLGPIFGSLLIFSTTKMGDNASLIDKLAD--AK 178 P+V L + A V V + G + P+ S LI + K +L D A Sbjct: 127 PYVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMAN 186 Query: 179 SVQMPYLGLAVFSLLLALIMYLLKLPDV--EKEMPKETTQ---KSLFSHKHFVFGALGIF 233 S+ PYLG+A+F +LAL + LP++ E E+ + T + K+ SH + FG + +F Sbjct: 187 SLVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAFGVIALF 246 Query: 234 FYVGGEVAIGSFLVLSFEKLLNLDSQSSAHYLV---YYWGGAMVGRFLGSVLMNK-IAPN 289 YV EV G + +F L ++ HY V Y ++G LG +L+ + I+ Sbjct: 247 VYVAVEVIAGD-TIGTFALSLGVE-----HYGVMTSYTMVCMVLGYTLGIILIPRFISQP 300 Query: 290 KYLAFNALSSIVLIALAIIIG---------------GKIA----LFALTFVGFFNSIMFP 330 L +A+ + L+ LAI+ G G +A L + F+G N+I++P Sbjct: 301 TALMISAILGL-LLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWP 359 Query: 331 TIFSLATLNLGHLTSKASGVISMAIVGGALIPPIQGAVTDMLTATESNLLYAYGVPLLCY 390 ++ LA LG LTS S ++ M I GGA P G + +AT+ Y V L CY Sbjct: 360 AVWPLALSGLGKLTSTGSALLIMGIAGGAFGPLFWGLTS---SATDMGQQGGYMVMLPCY 416 Query: 391 FYILFFALKGYK 402 +ILF+A+KG+K Sbjct: 417 LFILFYAVKGHK 428 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: 466 Number of extensions: 22 Number of successful extensions: 5 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: 432 Length adjustment: 32 Effective length of query: 375 Effective length of database: 400 Effective search space: 150000 Effective search space used: 150000 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: 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