Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_011881390.1 ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_000016205.1:WP_011881390.1 Length = 603 Score = 224 bits (571), Expect = 4e-63 Identities = 110/279 (39%), Positives = 176/279 (63%) Query: 5 LQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFVA 64 L +NGLI+G++YALLA+G +++G+ LINFAHG +YM+GAF+G+ + F + VA Sbjct: 5 LDYTLNGLIVGNIYALLAVGLALIFGVSHLINFAHGSVYMVGAFVGWLCLTRFGLPLPVA 64 Query: 65 LIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAFPQA 124 L + A LG+ IE + RPLRH+ RIA L+ IG+SF+L+ + + GA+ RA P Sbjct: 65 LAAVVAGCAALGIAIERIGLRPLRHAARIAPLLATIGISFILDQLVQLVFGADPRAVPTP 124 Query: 125 IQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLMGIN 184 + + +L + L+I GI + LL ++ T++G A+RA + D DAA MG++ Sbjct: 125 LPDWHVRIAGATLGALDLLIAGIGIAAAALLYGFLRFTRLGWAVRATAQDRDAALQMGVD 184 Query: 185 VNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGAALG 244 V+R FA+ AL G +G+L+ +YY+S++P MG LK VA ++GG+G +PGA G Sbjct: 185 VDRVNQAVFAIACALGGVSGLLVGMYYDSIDPAMGFQATLKGVVALLIGGLGNVPGAIAG 244 Query: 245 GFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGI 283 ++GL+E++ A + +RD +G+L++ L+ RP G+ Sbjct: 245 SLLLGLVESYGVALFGTSYRDLFAFGLLIVFLVWRPNGL 283 Score = 95.9 bits (237), Expect = 2e-24 Identities = 83/285 (29%), Positives = 138/285 (48%), Gaps = 18/285 (6%) Query: 4 MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFV 63 +LQ L N + Y LLAL T+V G + I+ H + ++GA+ L + + V Sbjct: 332 VLQTLTNAWL----YGLLALSLTLVAGTVGQISLGHAALLVIGAYASALLSSGLGWSPAV 387 Query: 64 ALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAFPQ 123 + A TA+LG ++ + A+R H IA L G+ ++ +V L P Sbjct: 388 TIPCAGAITAVLGTLLVYPAFRLRGHYVSIATL----GIGEVV--SLVILNWDGLTRGPL 441 Query: 124 AIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLMGI 183 I + L S L+++ LLQV + ++ +G+ +RAV D AA+ GI Sbjct: 442 GITGIA-PLPWASTARAAYWFALAVLVVLALLQVRLLRSHLGRTLRAVREDDVAARAHGI 500 Query: 184 NVNRTISFTFALGSALAGAAGVLIALYYNSL-EPLMGVTPGLKSFVAAVLGGIGIIPGAA 242 NR + FA+G AG +G + A Y+ + + + +LGG+G + G Sbjct: 501 APNRYKAIAFAVGGVAAGVSGGIAAHLYSYINHQTFDSQVSILALTMVILGGLGNVLGGI 560 Query: 243 LGGF-VIGLLETFATAFGMSDFRDAIVYGILLLILI-VRPAGILG 285 +G +IGL E F A +D+R ++YG++L++L+ RP G+LG Sbjct: 561 VGAVALIGLPELFRWA---ADYR-MLIYGVVLVLLVRFRPQGLLG 601 Lambda K H 0.330 0.146 0.407 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: 420 Number of extensions: 17 Number of successful extensions: 3 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: 292 Length of database: 603 Length adjustment: 32 Effective length of query: 260 Effective length of database: 571 Effective search space: 148460 Effective search space used: 148460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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