Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 150 bits (378), Expect = 7e-41 Identities = 95/263 (36%), Positives = 152/263 (57%), Gaps = 10/263 (3%) Query: 2 AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61 A P+L G+ K++ +T L +LYPGEI A++G NGAGKS++IK ++G + G Sbjct: 14 AAAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGG 73 Query: 62 EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121 ++RL G+ + SP+ A++ GI TVYQ + L P LS+A+N+F GR R G FR + Sbjct: 74 QMRLGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQG--FR-I 130 Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181 D A + ++AR ++ +GL ++ + + +Q VA+ARA + S+V+I+DEPT++ Sbjct: 131 DWATLHQRARDLVARIGLQI--DVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSS 188 Query: 182 LGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241 L E +++ E++ +R GL IV ++H + V+ V+DRI + R G + KD Sbjct: 189 LDDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQ 248 Query: 242 DAVAFMTG-----AKEPPREAIA 259 +A M G A E P A A Sbjct: 249 ALIAAMLGRDLAAASEQPAPAPA 271 Score = 97.8 bits (242), Expect = 4e-25 Identities = 64/228 (28%), Positives = 122/228 (53%), Gaps = 13/228 (5%) Query: 6 ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65 +L A GL G+ T L D + GE++ + G G+G++ + + + G PD G +R+ Sbjct: 279 LLQAEGL----GQDTQLQPLDLQIRAGEVVGLAGLLGSGRTELARLLFGLEQPDRGALRI 334 Query: 66 EGKPIQFRSPMEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLD 122 +G+ ++F +PM+A + G+ + + LS+ +N+ L + R +GK+ L Sbjct: 335 DGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVRENIALALQARMG--VGKF---LS 389 Query: 123 RAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAAL 182 R+ + A + LG+ T + +++ + LSGG +Q +AR A +++I+DEPT + Sbjct: 390 RSEQTELAERYVKLLGIKT-ETVDKPIGLLSGGNQQKAILARWMAIEPRLLILDEPTRGI 448 Query: 183 GVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRL 230 V + +++ IL + + G+ ++ IS M V VA RI + R R++ Sbjct: 449 DVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDRRKV 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: 282 Number of extensions: 7 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: 517 Length adjustment: 30 Effective length of query: 230 Effective length of database: 487 Effective search space: 112010 Effective search space used: 112010 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