Align 2-deoxy-D-ribonate transporter (characterized)
to candidate GFF2124 PS417_10835 major facilitator transporter
Query= reanno::Burk376:H281DRAFT_00642 (448 letters) >FitnessBrowser__WCS417:GFF2124 Length = 438 Score = 264 bits (674), Expect = 5e-75 Identities = 150/414 (36%), Positives = 233/414 (56%), Gaps = 9/414 (2%) Query: 24 RLIPLMCAIYFMSFLDRTNVALAKLQLAADVGISAAAYGFGSGIFFLGYALLEVPSNLAA 83 RL+PL+ Y ++LDR NV AKLQ+ +D+G+S AAYG G+GIFF+GY L E+PS L Sbjct: 23 RLLPLLFIGYVFAYLDRINVGFAKLQMQSDLGLSDAAYGAGAGIFFVGYVLFELPSTLML 82 Query: 84 HKVGPRRWIARIAVTWGILSTAMMFVQGTSSFYVLRVLLGIAEAGLFPALMYMVTLWFAP 143 ++G R+ +RI V WGI S M+FV+ +FY +R LLG+ EAG P ++Y ++ W+ P Sbjct: 83 PRIGARKTFSRILVLWGITSACMLFVRDVPTFYAMRFLLGVFEAGFAPGMIYYLSRWYGP 142 Query: 144 HDRPVVVGWIYIAPALALMLGNPLGGALM-QLDGFGGLHGWQWMFMLEGIPSVIVGIVLF 202 + ++IA + +LG P+ L+ G GGL GWQWMF++EG+P V +G++++ Sbjct: 143 SRMARAIAIVFIAGPMGGILGGPISAWLITTFAGVGGLAGWQWMFLIEGLPCVFLGVLMY 202 Query: 203 FKMPERPRDARWLSAAERDVLETHAVIDGHGRADYSSANWIAALKRPTTVLIGLIYFLNQ 262 + +RP DA WL+AAE+ +LET G A S ++ L+ P ++ YF Sbjct: 203 VVLCDRPADAPWLNAAEKQLLETEL-----GTASARSHSFRTVLRDPKLYVLASAYFCII 257 Query: 263 VAFVGLYFFTPAIIHQMHVDSSLVVGFLSASVGLGFLLGVLVLPRIHRRTDRDCVFLGIL 322 + + F+ PA+I + V+ + +G+ +A +G LG+ + R R + I Sbjct: 258 FSIYAMSFWLPAVIKALGVNDTQQLGWYAALPYVGAALGMYWIGRRSDRLGERRLHCAIP 317 Query: 323 TA-GLILGACAYLAVTNPAARIALLTVTAFFAGGVLPSYWAIAMKRLQGIQAAAGLAFVN 381 A G +L LA N +ALLT++ WA+ + ++G AA G+A +N Sbjct: 318 AATGAVLLILYPLAGGNLLVSMALLTLSISMMFMAYTVLWAMPSEHIKGEAAAGGIALIN 377 Query: 382 TIGLIGGFVGPYLFGIAETSSGRSDAGFTVILIAGVLGLALVPVLARAMRSEAG 435 TIGL GGF GP + G A+T++G D G +I + V A ++A R+ G Sbjct: 378 TIGLSGGFWGPAMIGWAKTATGSLDTG--LIAVGCVFLCAAFVIIATTPRTRTG 429 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: 577 Number of extensions: 28 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: 448 Length of database: 438 Length adjustment: 32 Effective length of query: 416 Effective length of database: 406 Effective search space: 168896 Effective search space used: 168896 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