Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS20740 Length = 503 Score = 165 bits (417), Expect = 2e-45 Identities = 91/245 (37%), Positives = 147/245 (60%), Gaps = 7/245 (2%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P+++ + L KR+ V AL F+L GE+ A++G+NGAGKS+++K ++G T D GEI Sbjct: 3 PLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEIL 62 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124 EG+P+ F+SP EA+ G+ ++Q L L L+IA NMF+GRE R G+ LD Sbjct: 63 YEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPR-----GRLGLFLDED 117 Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184 + QA L+ + + + V +L+ ++Q V +A+A +F S+V+IMDEPT+AL Sbjct: 118 KLNAQAHDILARMHVTL--DPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALND 175 Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244 E + +I D+++RG+ I+ ISH M + ++ADR+ + R G + + KD T+ + Sbjct: 176 AEIAELFRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAII 235 Query: 245 AFMTG 249 M G Sbjct: 236 GMMVG 240 Score = 80.9 bits (198), Expect = 5e-20 Identities = 59/205 (28%), Positives = 102/205 (49%), Gaps = 8/205 (3%) Query: 27 FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETV 86 F L GEIL G GAG++ + +A+ GA + GEI ++G R+P +A GI + Sbjct: 276 FALRKGEILGFAGLMGAGRTEVARAVFGADPIESGEIVVKGVKATIRNPSDAVARGIGYL 335 Query: 87 YQN---LALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQ 143 ++ L+ +S+ N+ + +RK + + R R + K A ++ L + T Sbjct: 336 SEDRKRFGLATGMSVESNIVMSN-LRKFLSLNFFLR---RTQIRKTAAHFINLLAIRT-P 390 Query: 144 NINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGLP 203 + Q V LSGG +Q + +A+ V+ DEPT + V + +L+ + +G Sbjct: 391 SATQEVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKA 450 Query: 204 IVLISHNMPHVFEVADRIHIHRLGR 228 IV+IS +P + ++DRI + GR Sbjct: 451 IVMISSELPEILRMSDRIVVMCEGR 475 Lambda K H 0.321 0.136 0.383 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: 289 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 503 Length adjustment: 29 Effective length of query: 231 Effective length of database: 474 Effective search space: 109494 Effective search space used: 109494 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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