Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Ac3H11_1109 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1109 Length = 513 Score = 139 bits (350), Expect = 1e-37 Identities = 86/246 (34%), Positives = 134/246 (54%), Gaps = 13/246 (5%) Query: 11 GLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPI 70 G+ KRY V A + PGEI AV+G+NGAGKS+++K I G+V PDEG + G+ + Sbjct: 2 GITKRYPAVVANSGVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQAV 61 Query: 71 QFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQA 130 Q R+P EAR GI V+Q+ +L L++A+N++LG + +SL A + ++ Sbjct: 62 QVRNPQEARALGIAMVFQHFSLFDTLTVAENVWLGLD-----------KSLTLAEVTQRI 110 Query: 131 RAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRV 190 AK +E GL I + + V TLS G+ Q V + RA KV+I+DEPT+ L + ++ Sbjct: 111 SAKAAEYGL-DIDPL-RPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKL 168 Query: 191 LELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTGA 250 ++ + G I+ ISH + + + + R G+ V NP + T + M GA Sbjct: 169 FVVLRKLASEGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGA 228 Query: 251 KEPPRE 256 + P E Sbjct: 229 EPPALE 234 Score = 70.9 bits (172), Expect = 5e-17 Identities = 59/250 (23%), Positives = 113/250 (45%), Gaps = 12/250 (4%) Query: 6 ILTARGLVKRYGRVTALDRAD--FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE-GE 62 +L +GL +D D F++ GE++ + G +G G+ ++ A+SG E Sbjct: 244 VLRVKGLSLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLYALSGEDQRAEPAS 303 Query: 63 IRLEGKPIQFRSPMEARQAGIETVYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFR 119 I++ G+ P + R G+ V + P + +A N+ L R+ G W + Sbjct: 304 IQVTGQNAGRMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTRKNAVGG--SGWIK 361 Query: 120 SLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPT 179 A++K A + + + A ++LSGG Q V R K++I+ +PT Sbjct: 362 V---GALQKHAEDIIQRFNVKA-GGPHSAAKSLSGGNLQKFIVGREIDANPKLLIVSQPT 417 Query: 180 AALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYT 239 + V + ++ IL +R G ++++S + +FE+ DR+H+ GR + + T Sbjct: 418 WGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSPSVQRAEAT 477 Query: 240 MSDAVAFMTG 249 + +M+G Sbjct: 478 VERIGEWMSG 487 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: 271 Number of extensions: 15 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: 513 Length adjustment: 29 Effective length of query: 231 Effective length of database: 484 Effective search space: 111804 Effective search space used: 111804 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