Align 2-deoxy-D-ribonate transporter (characterized)
to candidate BPHYT_RS05360 BPHYT_RS05360 MFS transporter
Query= reanno::Burk376:H281DRAFT_00642 (448 letters) >FitnessBrowser__BFirm:BPHYT_RS05360 Length = 439 Score = 280 bits (715), Expect = 9e-80 Identities = 151/403 (37%), Positives = 231/403 (57%), Gaps = 5/403 (1%) Query: 19 RKAMARLIPLMCAIYFMSFLDRTNVALAKLQLAADVGISAAAYGFGSGIFFLGYALLEVP 78 RK RL PL+ Y +++LDR NV AKLQ+ +D+G+S A YGFG+GIFF+GY + E+P Sbjct: 26 RKVSWRLAPLLMLCYVVAYLDRVNVGFAKLQMTSDLGLSDAVYGFGAGIFFVGYFIFEIP 85 Query: 79 SNLAAHKVGPRRWIARIAVTWGILSTAMMFVQGTSSFYVLRVLLGIAEAGLFPALMYMVT 138 SN+ HKVG R WIARI V+WG++S MFV + FYV+R LLG+AEAG FP ++ +T Sbjct: 86 SNVILHKVGARVWIARIMVSWGVISMLTMFVTTPTMFYVMRFLLGLAEAGFFPGIILYLT 145 Query: 139 LWFAPHDRPVVVGWIYIAPALALMLGNPLGGALMQ-LDGFGGLHGWQWMFMLEGIPSVIV 197 W+ H R + W A AL+ ++G P+ G +++ +G G HGWQW+F+LEGIPSVIV Sbjct: 146 YWYPAHRRGRMTTWFMTAIALSGVIGGPVSGYILKTFNGMNGWHGWQWLFLLEGIPSVIV 205 Query: 198 GIVLFFKMPERPRDARWLSAAERDVLETHAVIDGHGRADYSSANWIAALKRPTTVLIGLI 257 GI++F + +R A+WL+ E+ +LE H + + D L +++ L Sbjct: 206 GIMVFTMLDDRISKAKWLTKEEQQLLERHVSAEEATKHDMPIRQ---VLTSGRVLMLSLT 262 Query: 258 YFLNQVAFVGLYFFTPAIIHQMHVDSSLVVGFLSASVGLGFLLGVLVLPR-IHRRTDRDC 316 YF + G+ F+ P II V + ++G LSA G ++ ++ + R R+ +R Sbjct: 263 YFSFVMGLYGVSFWLPTIIKATGVTDAFMIGLLSAIPFAGAVVAMVFVSRSADRKRERRW 322 Query: 317 VFLGILTAGLILGACAYLAVTNPAARIALLTVTAFFAGGVLPSYWAIAMKRLQGIQAAAG 376 AG + + + N +A LT+ LP +W++ L G AAAG Sbjct: 323 HIALPAFAGAVGLVLSVVWAHNTVLAMASLTLATMGILTTLPLFWSLPTAILAGTGAAAG 382 Query: 377 LAFVNTIGLIGGFVGPYLFGIAETSSGRSDAGFTVILIAGVLG 419 +A +N+IG + GF+ PY G + ++ +D+G ++ VLG Sbjct: 383 IAMINSIGNLAGFLSPYAVGWLKQATAANDSGMYMLAAFMVLG 425 Lambda K H 0.329 0.142 0.436 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: 592 Number of extensions: 30 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: 448 Length of database: 439 Length adjustment: 32 Effective length of query: 416 Effective length of database: 407 Effective search space: 169312 Effective search space used: 169312 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 (21.8 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