Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate 206139 DVU0714 branched-chain amino acid ABC transporter, permease protein
Query= uniprot:A0A159ZYE0 (418 letters) >MicrobesOnline__882:206139 Length = 317 Score = 229 bits (584), Expect = 9e-65 Identities = 127/314 (40%), Positives = 191/314 (60%), Gaps = 26/314 (8%) Query: 96 LALIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSY 155 LA+++ L P F D+ I +Y +L L LN+++G AGL +G+ FYAVGAY+ Sbjct: 11 LAVLIAVL--PLFLDPYWTDVCVSIGLYAVLALSLNLILGQAGLFHMGHAAFYAVGAYTA 68 Query: 156 ALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRL-FLRNL 214 A+L+ + + +P+AG++AA F ++ P++ LRGDYL IVT+G EI+R+ + N+ Sbjct: 69 AILNTVYHVPVLWTMPVAGLLAALFALVVARPIIHLRGDYLLIVTIGIVEIVRIALINNV 128 Query: 215 TDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLAL 274 ITGG NGI I +P FG Y + F YL+ +A+ Sbjct: 129 FGITGGANGIFGISRPMLFG---------------------YKISKPIQFYYLIWTWVAI 167 Query: 275 AALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAAR 334 + L + RL GRA ++ED++A G++ KL+AF LGA +AG G+F+AA+ Sbjct: 168 SIL-LFRRLECSRFGRALNYIKEDDVAAEGSGVDTAYYKLAAFVLGALWAGMTGTFYAAK 226 Query: 335 QGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREFSEYRMLMFGAL 394 +++PESF+F ES ++ AIV+LGG GS GV+L A ++I LPE+ R+F+ RML+FG Sbjct: 227 MTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGLPELFRDFASARMLIFGLA 285 Query: 395 MVLMMIWRPQGLLP 408 MV+MMI+RPQG+LP Sbjct: 286 MVVMMIFRPQGMLP 299 Lambda K H 0.331 0.145 0.439 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: 413 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 418 Length of database: 317 Length adjustment: 29 Effective length of query: 389 Effective length of database: 288 Effective search space: 112032 Effective search space used: 112032 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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