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 AO353_25100 AO353_25100 glucose transporter
Query= TCDB::O25788 (407 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25100 Length = 425 Score = 282 bits (721), Expect = 2e-80 Identities = 163/394 (41%), Positives = 222/394 (56%), Gaps = 17/394 (4%) Query: 15 ALFFLMGFITVLNDILIPHLKPIFDLTYFEASLIQFCFFGAYFIMGGVFGNVISKIGYPF 74 +LFF++G IT LND+L+P LK +F L+Y EA L+Q FF AYFI G +IS+IGY Sbjct: 28 SLFFILGSITSLNDVLVPKLKHLFSLSYTEAMLVQSSFFFAYFIFAIPAGLLISRIGYMR 87 Query: 75 GVVLGFVITATGCALFYPAAHFGSYGFFLGALFILASGIVCLQTAGNPFVTLLSKGKEAR 134 VLG ++ A GC LF PA + FLGALF+LA G+ +Q NP ++LL A Sbjct: 88 AAVLGLLLMAGGCLLFIPATQSALFPAFLGALFVLAIGVTTVQVVANPLLSLLGTAATAP 147 Query: 135 N-LVLVQAFNSLGTTLGPIFGSLLIFSTTKMGDNASLIDK------LADAKSVQMPYLGL 187 + L L AFNSLGTT+ P G++LI + D ++L +A + Y + Sbjct: 148 SRLTLGHAFNSLGTTVAPYLGAILILGSLNAVDTSALSPAELTSFLSQEASVISNTYASI 207 Query: 188 AVFSLLLALIMYLLK---LPDVEKEMPKETTQKSLFSHKHFVFGALGIFFYVGGEVAIGS 244 +F ++ALI++L + P E +L F G IF YVG EV IGS Sbjct: 208 TLFICMVALIVWLKRNELQPSTRPERLNPLAALNLLKQPRFALGTASIFLYVGAEVTIGS 267 Query: 245 FLV--LSFEKLLNLDSQSSAHYLVYYWGGAMVGRFLGSVLMNKIAPNKYLAFNALSSIVL 302 + L L L ++++ ++ +YWGGA+VGRF+GS LM AP K LAF A + IVL Sbjct: 268 LITDYLMLPTTLALPAEAAGKHVAFYWGGALVGRFIGSALMRTFAPGKLLAFAATAVIVL 327 Query: 303 IALAIIIGGKIALFALTFVGFFNSIMFPTIFSLATLNLGHLTSKASGVISMAIVGGALIP 362 + ++ G +A ++L VG FNSIMFPTIF+LAT LGH ++ SG+ AIVGGA IP Sbjct: 328 LTISATTQGVVAGWSLLAVGLFNSIMFPTIFTLATAGLGHRAAEGSGLFCCAIVGGAFIP 387 Query: 363 PIQGAVTDMLTATESNLLYAYGVPLLCYFYILFF 396 P+ G D+ S L A VP CY I + Sbjct: 388 PLTGYAADL-----STLAMALSVPATCYACIAIY 416 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: 464 Number of extensions: 26 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: 407 Length of database: 425 Length adjustment: 31 Effective length of query: 376 Effective length of database: 394 Effective search space: 148144 Effective search space used: 148144 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