Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 127 bits (320), Expect = 4e-34 Identities = 80/227 (35%), Positives = 123/227 (54%), Gaps = 20/227 (8%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P++ G+ K +G V A D+ PG I A++G+NGAGKS+++ +SG + D G I Sbjct: 33 PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIH 92 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFR--SLD 122 ++G+ ++FRSP +A +AGI VYQ+ L ++++A+N+ LG+ G W + Sbjct: 93 VDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS-------GAWLSPVHMS 145 Query: 123 RAAMEKQARAKLSELGLMTIQNINQAVET--LSGGQRQGVAVARAAAFGSKVVIMDEPTA 180 R E AR L +I+ A LS G+RQ V + + S+V+I+DEPTA Sbjct: 146 RVVAELAARYGL---------DIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTA 196 Query: 181 ALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLG 227 L E+ ++ E + + G IV ISH M V +AD I I R G Sbjct: 197 VLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRG 243 Score = 75.1 bits (183), Expect = 3e-18 Identities = 62/227 (27%), Positives = 105/227 (46%), Gaps = 16/227 (7%) Query: 27 FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKP-IQF--RSPMEARQAGI 83 F++ GE+ A+ G G G+ +++ ++G P EGE+ L G P QF ++P + A I Sbjct: 300 FEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYI 359 Query: 84 ETVYQNLALSPALSIADNMFL---GREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLM 140 Q LA +L + DN L G R P LDR + + AR L+E + Sbjct: 360 PEDRQGLATCLSLDLVDNFLLTARGCFTRGP--------FLDRKSADAAARDILAEYNVQ 411 Query: 141 TIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRR 200 +LSGG Q + V R +++ + PT L + + V +L+VR Sbjct: 412 P-GRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSH 470 Query: 201 GLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFM 247 ++L+S ++ V +ADR+ + G + +++ D DA+ M Sbjct: 471 A-GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLM 516 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: 315 Number of extensions: 14 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: 524 Length adjustment: 30 Effective length of query: 230 Effective length of database: 494 Effective search space: 113620 Effective search space used: 113620 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 Apr 09 2024. 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