Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate H281DRAFT_00211 H281DRAFT_00211 D-galactonate transporter
Query= reanno::Koxy:BWI76_RS23715 (445 letters) >FitnessBrowser__Burk376:H281DRAFT_00211 Length = 439 Score = 299 bits (765), Expect = 1e-85 Identities = 148/415 (35%), Positives = 240/415 (57%), Gaps = 7/415 (1%) Query: 15 QRTHKKIYRHLMPLLIVAYIISFIDRTNIGMAKATMSVDIGLSATAFGLGAGLFFLTYAV 74 + T++K+ L PLL++ Y+++++DR N+G AK M+ D+GLS +G GAG+FF+ Y Sbjct: 22 EATYRKVNWRLAPLLMLCYVVAYLDRVNVGFAKLQMTSDLGLSDAVYGFGAGIFFVGYFF 81 Query: 75 LEIPSNLFLTRIGARRWIARIMITWGIISCGMAFVTGPTSFYVMRLLLGAAEAGLYPGII 134 EIPSN+ L ++GAR WIARIM++WG+IS FVT PT FYVMR LLG AEAG +PGII Sbjct: 82 FEIPSNVILHKVGARVWIARIMVSWGVISMLTMFVTTPTMFYVMRFLLGVAEAGFFPGII 141 Query: 135 YYLTLWFGREERAKATGLFLLGVCLANIIGAPLGGLLL-SLDGMSGWHGWQWMFFIEGLP 193 YLT W+ R + T F+ + L+ +IG P+ G +L + +GM+GWHGWQW+F +EG+P Sbjct: 142 LYLTYWYPSHRRGRMTTWFMTAIALSGVIGGPVSGYILKTFNGMNGWHGWQWLFLLEGIP 201 Query: 194 AIALAFVVWRRLPDKPADARWLDSHDVQAITAVLEKEAEETRHTPSRFSLKTALTTRVFL 253 ++ + +V+ L D+ + A+WL + + +LE+ T ++ LT+ L Sbjct: 202 SVLVGILVFVALDDRISKAKWLTKEEKE----LLERHVSAEEATKHDMPIRQVLTSGRVL 257 Query: 254 LLVLIYFTHQFSVYGLSYFLPGIIGSWGQLTPLQIGLLTAIPWIAAAAGGILLPRFARTE 313 +L YF+ +YG+S++LP II + G IGLL+A+P+ AA + + R A Sbjct: 258 MLSFTYFSFVMGLYGVSFWLPTIIKATGVTDAFAIGLLSAVPFAAAVVAMVFVARSADRT 317 Query: 314 QRSRSMLMAGYLVMATGMAIGAIAGHG--VALLGFSLAAFMFFAMQSIIFNWLPSIMSGH 371 + R + A G+ + + +A+ +LA + ++ +I++G Sbjct: 318 RERRWHIALPAFAGAIGLVLSVVWAQNTLLAMASLTLATMGILTTLPLFWSLPTAILAGT 377 Query: 372 MLAGSFGLLNCLGLCGGFLGPFILGAFEDRTGAATSGLWFAVALLIVGALASLLI 426 A ++N +G GFL P+ +G + T A SG++ A ++VG L ++ + Sbjct: 378 GAAAGIAMINSIGNLAGFLSPYAVGWLKQATAANDSGMYMLAAFMVVGGLLAISV 432 Lambda K H 0.328 0.141 0.438 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: 517 Number of extensions: 24 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: 445 Length of database: 439 Length adjustment: 32 Effective length of query: 413 Effective length of database: 407 Effective search space: 168091 Effective search space used: 168091 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