Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 151 bits (382), Expect = 2e-41 Identities = 89/249 (35%), Positives = 139/249 (55%), Gaps = 8/249 (3%) Query: 3 QEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGE 62 Q P+L G+VK + V ALD + PGE+ A++G+NGAGKS+++K + G PDEG+ Sbjct: 4 QSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQ 63 Query: 63 IRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLD 122 I + +P+ P++A+ GI ++Q L+L+ LS+A+N++LG RK F +D Sbjct: 64 IIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKR------FGLVD 117 Query: 123 RAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAAL 182 A +E + A L +L + N V LS +Q V +ARA +K VI DEPTA+L Sbjct: 118 WAELEAKTNAILEKLKVGF--NAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASL 175 Query: 183 GVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSD 242 E + E+I D++ +G+ I ISH M +F++ DRI + R G+ +N + + Sbjct: 176 TDAEKVVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEEN 235 Query: 243 AVAFMTGAK 251 M G K Sbjct: 236 VTQMMIGRK 244 Score = 85.1 bits (209), Expect = 3e-21 Identities = 62/227 (27%), Positives = 106/227 (46%), Gaps = 9/227 (3%) Query: 26 DFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIET 85 +F++ GE++ G GAG++ + + + G P G I L+G + SP +A + GI Sbjct: 276 NFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISL 335 Query: 86 VYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTI 142 V ++ L ++ DNM L + G + A+ Q R KL + Sbjct: 336 VPEDRKGQGLVLGMNCRDNMTLPQVDDLKA--GPFVADGAEIAIFDQYRDKLD----IRT 389 Query: 143 QNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGL 202 Q V LSGG +Q + + + + V+I+DEPT + V + L+ D+ +G Sbjct: 390 PGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGY 449 Query: 203 PIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTG 249 +++IS MP V VADRI GR + ++ T + +A ++G Sbjct: 450 AVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISG 496 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: 280 Number of extensions: 17 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