Align gluconate:H+ symporter (gntT) (characterized)
to candidate N515DRAFT_2225 N515DRAFT_2225 gluconate permease GntT (TC 2.A.8.1.4)
Query= reanno::Cup4G11:RR42_RS28835 (453 letters) >FitnessBrowser__Dyella79:N515DRAFT_2225 Length = 457 Score = 613 bits (1580), Expect = e-180 Identities = 306/449 (68%), Positives = 370/449 (82%), Gaps = 5/449 (1%) Query: 6 GTTLLLYALIAVIALVVLIAKFKLNPFITLVVVSVLLGFAVGMPMGDIVKSFEAGVGGTL 65 G LLL A +AV+ L+ LIA KLNPF+ L++VS+ LG AVGMPM IVK+FE G GGTL Sbjct: 12 GDALLLAAALAVVVLIYLIAALKLNPFVALLMVSLGLGVAVGMPMKGIVKAFETGAGGTL 71 Query: 66 GHIALVVGLGTMLGKMMAESGGAERIARTLIDAFGEKNVHWAMVTIAFIVGLPVFFEVGF 125 GHIAL++ LGTMLGKMMAESGG ERIA TLI AFGE+ HWAM+T+AFIVGLPVFF+VGF Sbjct: 72 GHIALLIALGTMLGKMMAESGGTERIAHTLIAAFGERRAHWAMMTVAFIVGLPVFFDVGF 131 Query: 126 VLLVPIAFNVAKRTGTSMVLVGIPMVAGLSVVHGLIPPHPAALLAVTAYKADIGKTILYA 185 VLLVP+AF++AKR G ++L+G+ M AGLSVVHGL+PPHPAALLAVTAY+ADIGKTILYA Sbjct: 132 VLLVPVAFHIAKRAGMPLLLIGLSMSAGLSVVHGLVPPHPAALLAVTAYQADIGKTILYA 191 Query: 186 LIVGIPTAAIAGPLFAKLMTRYVTLPDVNPLAAQFTEEDEGVKASHELPGFGITLFTILL 245 +++G+PTA IAGPLFA+ +TRYVT+ NPL +F E D+ +LP FGI L T+LL Sbjct: 192 VLIGLPTAIIAGPLFARWVTRYVTVEAENPLEKEFVEIDQ----ERQLPSFGIALATLLL 247 Query: 246 PVILMLIGSWADLITTPKTFANDFLKLIGNSVIALLIAALVSFYTFGKRRGFTRENILRF 305 PV+LML+G+WADL++TP + AN L +GN V+ALL+A L+SFYTFGKRRGF+RE IL F Sbjct: 248 PVLLMLVGTWADLLSTPGSRANAVLGFLGNPVVALLVAVLLSFYTFGKRRGFSRETILGF 307 Query: 306 TNECVAPTAIITLVVGAGGGFGRVLRDSGISNAIVDVATGAHVSVLLLGWLVAVLIRIAT 365 TN+C+APTA + LVVGAGGGFGR+L DSG+S+AI+ + +S LLLGWL+A L+RIAT Sbjct: 308 TNDCLAPTATVILVVGAGGGFGRILLDSGVSHAIIGATQSSQISPLLLGWLIAALLRIAT 367 Query: 366 GSATVAMTTAAGIVAPIAASV-PGTRPELLVLTTGAGSLILSHVNDGGFWLVKEYFNMTV 424 GSATVAM TA GIVAPIAA+ PEL+VL TGAGSLILSHVNDGGFW+VK+YFNMTV Sbjct: 368 GSATVAMGTACGIVAPIAAAASKAVHPELMVLATGAGSLILSHVNDGGFWIVKQYFNMTV 427 Query: 425 AQTFKTWSVCETLISVIALLLTLALATVV 453 QT KTW+V ET+ISV+ALLLTL LA V+ Sbjct: 428 TQTLKTWTVLETIISVVALLLTLGLAAVL 456 Lambda K H 0.326 0.141 0.410 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: 813 Number of extensions: 53 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: 453 Length of database: 457 Length adjustment: 33 Effective length of query: 420 Effective length of database: 424 Effective search space: 178080 Effective search space used: 178080 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 (21.6 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