Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate RR42_RS20120 RR42_RS20120 amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__Cup4G11:RR42_RS20120 Length = 383 Score = 186 bits (472), Expect = 9e-52 Identities = 116/360 (32%), Positives = 188/360 (52%), Gaps = 9/360 (2%) Query: 11 LFAAMAIAGFASYSMA---ADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGG-V 66 L A+++AG + S A A IK+ A P+TG AQYG + G ++AIE++N + Sbjct: 10 LTVALSVAGLCATSAAFAQAQEIKLGFAAPMTGGQAQYGKDMQNGVVLAIEEMNATKPKI 69 Query: 67 NGAQLEGVIY--DDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMI 124 G ++ V+ DDA DPK VA K+V++G++ ++GH S ++ PA+ +Y G+ I Sbjct: 70 GGKDVKFVLLSEDDAADPKTGSVVAQKLVDNGIQGMLGHFNSGTSIPASMVYNRAGIPQI 129 Query: 125 TPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATE 184 ATAPE T +G+K FR + D QG V G F+ ++ K IA++ D+ YG+G+A E Sbjct: 130 A-MATAPEYTRQGFKTTFRMMTSDTQQGSVIGAFVVKKLGAKNIAIVDDRTAYGQGLADE 188 Query: 185 VKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAG 244 +K + AG K+ E N DF A+++ +K++ ++FGG + + +Q K+ G Sbjct: 189 FEKAAKAAGGKIVRREFTNDKAVDFKAVLTNIKRSNPDVIFFGGAETQSAPMAKQVKELG 248 Query: 245 LDARFMGPEGVGNSEITAIAGDASEGMLATLP-RAFEQDPKNKALIDAFKAKNQDPSGIF 303 + + + E +AG A+EG + +L EQ P A ++ + + Sbjct: 249 MKSPVVSGEMSKTDNFLKLAGPAAEGTVVSLAGLPLEQMPGGTAYEKKYEKRFGSKVQTY 308 Query: 304 VLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFE-TPTGNLGFDEKGDLKNFDFTVYE 362 AY T + + KAG ADP + L A + T L +D +GDLK+ TVY+ Sbjct: 309 SPYAYDGATALMTAMIKAGSADPARYLPVLAATNMQGVTTKTLAYDARGDLKDGGITVYK 368 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: 360 Number of extensions: 14 Number of successful extensions: 5 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: 373 Length of database: 383 Length adjustment: 30 Effective length of query: 343 Effective length of database: 353 Effective search space: 121079 Effective search space used: 121079 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