Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate PP_3176 PP_3176 Major facilitator family transporter
Query= reanno::Koxy:BWI76_RS23715 (445 letters) >FitnessBrowser__Putida:PP_3176 Length = 440 Score = 270 bits (689), Expect = 9e-77 Identities = 154/433 (35%), Positives = 235/433 (54%), Gaps = 9/433 (2%) Query: 11 GTQLQRT--HKKIYRHLMPLLIVAYIISFIDRTNIGMAKATMSVDIGLSATAFGLGAGLF 68 GT R +++I L+P + + Y+ +++DR N+G AK M + S T +GLGAG+F Sbjct: 10 GTDTTRNALYRRITLRLIPFIFICYLFNYLDRVNVGFAKLQMLDALKFSETVYGLGAGIF 69 Query: 69 FLTYAVLEIPSNLFLTRIGARRWIARIMITWGIISCGMAFVTGPTSFYVMRLLLGAAEAG 128 F+ Y + +PSNL L R G RRWIA +MI WG +S + FVT PT FY +RLL GAAEAG Sbjct: 70 FIGYVLCGLPSNLALNRFGPRRWIALMMIAWGSLSTCLLFVTTPTEFYTLRLLTGAAEAG 129 Query: 129 LYPGIIYYLTLWFGREERAKATGLFLLGVCLANIIGAPLGGLLLS--LDGMSGWHGWQWM 186 +PG++ YL+ WF R + LF+ + ++ ++G P G +L G G GWQWM Sbjct: 130 FFPGVVLYLSRWFPAARRGRIMALFMSAIPVSGLLGGPFSGWILEHFAAGQHGLAGWQWM 189 Query: 187 FFIEGLPAIALAFVVWRRLPDKPADARWLDSHDVQAITAVLEKEAEETRHTPSRFSLKTA 246 F I+GLP +AL + L D A WL + Q I A L+ +A T S S+ Sbjct: 190 FLIQGLPTVALGVLAVFLLSDGYQKAAWLSPAERQLIAADLQADAASKPSTTSD-SVLAV 248 Query: 247 LTTRVFLLLVLIYFTHQFSVYGLSYFLPGIIGSWGQLTPLQIGLLTAIPWIAAAAGGILL 306 LT + +YF Q VY ++++LP II + PL IG L+AIP++ A IL Sbjct: 249 LTNPLIWTFGFVYFCIQSGVYAINFWLPSIIKGFD--NPLLIGWLSAIPYLLAGVFMILC 306 Query: 307 PRFARTEQRSRSMLMAGYLVMATGMAIGA-IAGH-GVALLGFSLAAFMFFAMQSIIFNWL 364 R A R L+ L+ A G+ I AG+ +A+LG S+A + + Sbjct: 307 GRSADLRNERRWHLVVPMLMGAVGLLIAVNFAGNPTIAILGLSIATMGALTGLPMFWPMP 366 Query: 365 PSIMSGHMLAGSFGLLNCLGLCGGFLGPFILGAFEDRTGAATSGLWFAVALLIVGALASL 424 +++S ++N +G GFL P+++G +D+TG+ + L+ AL+++G+L +L Sbjct: 367 TALLSAGAAVAGLAIINSVGQMAGFLSPYLVGFIKDQTGSTDAALYSLAALIVLGSLVAL 426 Query: 425 LIKSSSSSTPASA 437 + + S + A A Sbjct: 427 RVTRAGSLSTARA 439 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: 482 Number of extensions: 20 Number of successful extensions: 3 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: 440 Length adjustment: 32 Effective length of query: 413 Effective length of database: 408 Effective search space: 168504 Effective search space used: 168504 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