Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate RR42_RS16980 RR42_RS16980 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__Cup4G11:RR42_RS16980 Length = 401 Score = 207 bits (526), Expect = 5e-58 Identities = 116/345 (33%), Positives = 188/345 (54%), Gaps = 5/345 (1%) Query: 30 IKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG-GVNGAQ--LEGVIYDDACDPKQAV 86 +KI A P+TG +A G GA +A+E++NK G +NG + LE V DDA DPK Sbjct: 51 VKIGHAAPLTGGIAHLGKDNENGARLAVEEVNKTGLEINGKKIKLELVGEDDAGDPKTGT 110 Query: 87 AVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPEITSRGYKLIFRTIG 146 AVA K+V+ V VVGH+ S + PA+ IY D G++ I+PS+T P+ T +G+K FR + Sbjct: 111 AVAQKLVDAKVVAVVGHLNSGVSIPASKIYSDAGIVQISPSSTNPDYTKQGFKTTFRVVA 170 Query: 147 LDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDAGIKVAVFEGLNAGD 206 D QGP + + K++A++ D YG+G+A E +KT + +G+ V E N Sbjct: 171 TDAQQGPALANYATKSLHAKSVAIVDDATAYGKGLADEFEKTAKASGVNVVAREATNDKA 230 Query: 207 KDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFMGPEGVGNSEITAIAGD 266 DF A+++K+K + +GG G +QAK+ G+ ++ +G +GV ++ +AGD Sbjct: 231 TDFKAILTKIKGKKPDVIMYGGMDATGGPFAKQAKELGISSKIVGGDGVCTDKVAELAGD 290 Query: 267 ASEGMLAT-LPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAVTVIAKGIEKAGEAD 325 A ++ + A + + ++A+ P I+ Y AV VI +++A + Sbjct: 291 AVSNIICSEAGLALSKMEQGADFDKRYQARFNAPVQIYAPFTYDAVMVIVDAMKRANSTE 350 Query: 326 PEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKDATRT 370 P + + ++ GN+ FDEKGD+K T+YE +KD +T Sbjct: 351 PAAILAEMPKTNYKGLIGNIAFDEKGDMKEGTITLYE-YKDKKKT 394 Score = 23.9 bits (50), Expect = 0.008 Identities = 14/46 (30%), Positives = 17/46 (36%) Query: 126 PSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVL 171 P+A E+ YK + I D G YKDK VL Sbjct: 351 PAAILAEMPKTNYKGLIGNIAFDEKGDMKEGTITLYEYKDKKKTVL 396 Lambda K H 0.316 0.133 0.377 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: 423 Number of extensions: 23 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: 373 Length of database: 401 Length adjustment: 30 Effective length of query: 343 Effective length of database: 371 Effective search space: 127253 Effective search space used: 127253 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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