Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate HSERO_RS05320 HSERO_RS05320 ribonucleotide-diphosphate reductase subunit alpha
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__HerbieS:HSERO_RS05320 Length = 502 Score = 155 bits (392), Expect = 2e-42 Identities = 90/256 (35%), Positives = 146/256 (57%), Gaps = 12/256 (4%) Query: 6 ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65 +L G+ K +G VT L D ++ GE+ A++G+NGAGKS+++K + G V PD GEIR+ Sbjct: 1 MLQLTGIKKNFGPVTVLRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPDAGEIRI 60 Query: 66 EGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAA 125 +G+P +F S A G+ V+Q +L P L DNMFL RE+R +W L RAA Sbjct: 61 DGQPCRFDSYRAAIAGGVGVVFQEFSLIPYLDAVDNMFLARELR-----SRW-GWLQRAA 114 Query: 126 MEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVK 185 M ++A+ + +LG+ ++ V LS Q+Q V +A+A A ++++++DEPTA L Sbjct: 115 MRRRAQEIIGQLGVAI--PLDVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPA 172 Query: 186 ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVA 245 E + ++ +R +G+ I+ ISH++ +FE+ DRI + R G + + + V Sbjct: 173 EVEHLFAVMRSLRAQGVAIIFISHHLEEIFEICDRITVLRDGAYVATCATAEVDQARLVE 232 Query: 246 FMTGAK----EPPREA 257 M G + PP+ A Sbjct: 233 MMVGRRIENCFPPKPA 248 Score = 85.9 bits (211), Expect = 2e-21 Identities = 62/208 (29%), Positives = 102/208 (49%), Gaps = 12/208 (5%) Query: 25 ADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIE 84 + F L GEIL G G+G++ + A+ GA ++ + G P++F P +A QAGI Sbjct: 273 SQFQLRRGEILGFAGLVGSGRTETVLAMLGAHAALSCKLSMHGVPLRFADPAQALQAGIG 332 Query: 85 TVYQNL---ALSPALSIADNMFLGR--EIRKPGIMGKWFRSLDRAAMEKQARAKLSELGL 139 + ++ L + SI N+ L + R G+ LDR ++ A + + + Sbjct: 333 LLPESRKEQGLITSFSILHNVSLNNYGKYRLGGLF------LDRRREQQATEAAMQRVRV 386 Query: 140 MTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRR 199 V+TLSGG +Q V +AR KV+I DEPT + V + +L+ + Sbjct: 387 KA-PGAQVRVDTLSGGNQQKVVIARWINHAMKVLIFDEPTRGIDVGAKSEIYQLMREFTA 445 Query: 200 RGLPIVLISHNMPHVFEVADRIHIHRLG 227 +G I++IS +P V +ADR+ + R G Sbjct: 446 QGYSILMISSELPEVVGMADRVCVFRGG 473 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: 292 Number of extensions: 18 Number of successful extensions: 5 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: 502 Length adjustment: 29 Effective length of query: 231 Effective length of database: 473 Effective search space: 109263 Effective search space used: 109263 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