Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__BFirm:BPHYT_RS20740 Length = 503 Score = 347 bits (890), Expect = e-100 Identities = 185/476 (38%), Positives = 301/476 (63%), Gaps = 10/476 (2%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P++ +K ++ FPGV+AL V L GEVHALMGENGAGKST++K L GVY + G I+ Sbjct: 3 PLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEIL 62 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGI--DWKKTHEA 123 +G+P F +AQ G+ ++QE+ L +L++ +N+ +G E RG G+ D K + Sbjct: 63 YEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLNAQ 122 Query: 124 AKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDL 183 A LA+M + ++DP +SS+++A QQ+V IA+A+ +++VLI+DEPTS+L+ E+ +L Sbjct: 123 AHDILARMHV-TLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAEL 181 Query: 184 FAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGK 243 F I+R ++ GV I+++SH +D++ +I DR+T+LR+G+++ V KDT +IGMM+G+ Sbjct: 182 FRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGR 241 Query: 244 SAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303 + + A ++ GE + +V L + V + KGE++GFAGL+G+GRT Sbjct: 242 TLTD-----AAPSQHIANQGEVAL-EVTRLNAGPLVRDVSFALRKGEILGFAGLMGAGRT 295 Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363 E+ R ++GAD +SG + G K I +P A+ I Y +E+R+ G+ ++V NI+ Sbjct: 296 EVARAVFGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIV 355 Query: 364 IA-LQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLAT 422 ++ L+ + + + + ++ L +R + V+ LSGGNQQK++I +WL Sbjct: 356 MSNLRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLER 415 Query: 423 HPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478 ++L DEPTRGID+GAK+EI +++ LA QG +V ISSEL E++R+SD I V+ Sbjct: 416 DCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVM 471 Score = 95.1 bits (235), Expect = 5e-24 Identities = 63/244 (25%), Positives = 123/244 (50%), Gaps = 8/244 (3%) Query: 266 PIVDVKGLGKK----GTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321 P++ VK L K+ ++ V ++ GEV G G+G++ L ++L G D+G Sbjct: 3 PLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEIL 62 Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEA 381 G+ V+ P A + + + ++ LT+ QN+ I + + + + + Sbjct: 63 YEGQPVDFQSPREAQAVGVGIIHQELQ---LMNHLTIAQNMFIGREPRGRLGLFLDEDKL 119 Query: 382 DAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAK 441 +A + ++V DP V +L+ QQ V I + L+ +LI+DEPT ++ Sbjct: 120 NAQAHDILARMHVT-LDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEI 178 Query: 442 AEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVET 501 AE+ +++ DL +G+G+++IS +++E+ +++D + VL+D +A + DT QA I Sbjct: 179 AELFRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMM 238 Query: 502 IANT 505 + T Sbjct: 239 VGRT 242 Score = 78.6 bits (192), Expect = 5e-19 Identities = 50/218 (22%), Positives = 103/218 (47%), Gaps = 6/218 (2%) Query: 26 VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIA 85 V L GE+ G GAG++ + +A+ G I +G I+V G DA GI Sbjct: 274 VSFALRKGEILGFAGLMGAGRTEVARAVFGADPIESGEIVVKGVKATIRNPSDAVARGIG 333 Query: 86 TVYQE---VNLCTNLSVGENVMLGHEKRG---PFGIDWKKTHEAAKKYLAQMGLESIDPH 139 + ++ L T +SV N+++ + ++ F + + + A ++ + + + Sbjct: 334 YLSEDRKRFGLATGMSVESNIVMSNLRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSAT 393 Query: 140 TPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILF 199 + +S QQ + IA+ + + VL DEPT +D +++ ++R + D G AI+ Sbjct: 394 QEVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVM 453 Query: 200 VSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237 +S L +I ++DR+ ++ G+ E+ ++ ++ Sbjct: 454 ISSELPEILRMSDRIVVMCEGRITGELAAAGATQERIM 491 Lambda K H 0.316 0.135 0.376 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: 26 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 513 Length of database: 503 Length adjustment: 34 Effective length of query: 479 Effective length of database: 469 Effective search space: 224651 Effective search space used: 224651 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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