Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate 350090 BT0562 putative ABC transporter ATP-binding protein (NCBI ptt file)
Query= CharProtDB::CH_003736 (237 letters) >FitnessBrowser__Btheta:350090 Length = 489 Score = 109 bits (273), Expect = 9e-29 Identities = 73/219 (33%), Positives = 121/219 (55%), Gaps = 10/219 (4%) Query: 10 KVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVFDDKDI 69 ++S YGK++AL EVS + QGE+ LIG +GAGK+TL L A G + D+ Sbjct: 12 EISKSYGKVEALKEVSFAVEQGEVFGLIGPDGAGKSTLFRILTTLLLADKGTATVNGLDV 71 Query: 70 -TDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAE--RDQFQERIKWVYELFPR 126 TD+ K +R V +P ++ ++VEENL FFA QE + +++ + Sbjct: 72 VTDY---KQIRTKVGYMPGRFSLYQDLSVEENLE---FFATVFHTLIQENYDLIKDIYQQ 125 Query: 127 LHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLREQ 186 + + +RAG +SGG +Q LA+ +L+ P +L LDEP+ G+ P+ ++ + + LR+Q Sbjct: 126 IEPFKKRRAGALSGGMKQKLALSCSLIHKPDILFLDEPTTGVDPVSRKEFWQMLRNLRKQ 185 Query: 187 GMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALL 225 G+TI + ++A + DR + +G V DT + +L Sbjct: 186 GITIIVSTPIMDEA-RQCDRIAFINHGQVHGIDTPERIL 223 Score = 82.8 bits (203), Expect = 1e-20 Identities = 58/224 (25%), Positives = 116/224 (51%), Gaps = 10/224 (4%) Query: 1 MEKVMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSG 60 M ++ ++++ +G A+ +S + +GEI +GANGAGKTT + LCG R TSG Sbjct: 243 MAAPVIEVEQLTKSFGHFTAVDHISFQVQRGEIFGFLGANGAGKTTAMRMLCGLSRPTSG 302 Query: 61 RIVFDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAM-GGFFAERD-QFQERIK 118 DI ++ A+ ++ + + + ++ + V EN+ + G + ++ + +E+ Sbjct: 303 VGKVAGYDI--FREAEQVKRHIGYMSQKFSLYEDLKVWENIRLFAGIYGMKEMEIEEKTD 360 Query: 119 WVYELFPRL--HERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQI 176 EL RL + R + G +Q LA ++ P+++ LDEP+ G+ P +Q Sbjct: 361 ---ELLERLGFADERDTLVKNLPLGWKQKLAFSVSIFHEPKIVFLDEPTGGVDPATRRQF 417 Query: 177 FDTIEQLREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDT 220 ++ I Q ++G+T+F+ ++A + +R ++ +G + DT Sbjct: 418 WELIYQAADRGITVFVTTHYMDEA-EYCNRISIMVDGQIKALDT 460 Lambda K H 0.321 0.137 0.390 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: 251 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: 237 Length of database: 489 Length adjustment: 28 Effective length of query: 209 Effective length of database: 461 Effective search space: 96349 Effective search space used: 96349 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