Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 Length = 514 Score = 131 bits (330), Expect = 2e-35 Identities = 73/222 (32%), Positives = 130/222 (58%), Gaps = 9/222 (4%) Query: 7 LTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLE 66 L G+ K + V ALD F +PG++ A++G+NGAGKS+++K + GA TP G +++ Sbjct: 16 LRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIG 75 Query: 67 GKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAM 126 + + F+S ++ +G+ ++Q L L P +++A+N+FLG + F ++R+ + Sbjct: 76 ERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGH-------LPASFGLINRSTL 128 Query: 127 EKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKE 186 +QA A L GL + + V LS GQRQ V +A+A + G+ V+ DEPT++L +E Sbjct: 129 RQQALACLK--GLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSARE 186 Query: 187 SRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGR 228 R++ +I +R G ++ +SH M VF + + + + + GR Sbjct: 187 IDRLMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGR 228 Score = 85.5 bits (210), Expect = 2e-21 Identities = 56/199 (28%), Positives = 104/199 (52%), Gaps = 10/199 (5%) Query: 27 FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETV 86 F+++ GEIL + G GAG++ +++ +SG G+++L G ++ RSP +A AGI Sbjct: 285 FEVHKGEILGLFGLVGAGRTELLRLLSGLARHSAGQLKLRGHELKLRSPRDAIAAGILLC 344 Query: 87 YQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQ-ARAKLSELGLMTI 142 ++ + P S+A+N+ I G F L R EK A ++ L + T Sbjct: 345 PEDRKKEGILPLASVAENI----NISARGAHST-FGCLLRGLWEKDNAEQQIKALKVKT- 398 Query: 143 QNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGL 202 N Q + LSGG +Q + R + KV+++DEPT + + + ++I ++ G+ Sbjct: 399 PNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGI 458 Query: 203 PIVLISHNMPHVFEVADRI 221 ++++S ++ V ++DRI Sbjct: 459 AVIVVSSDLMEVMGISDRI 477 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: 287 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: 514 Length adjustment: 29 Effective length of query: 231 Effective length of database: 485 Effective search space: 112035 Effective search space used: 112035 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