Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate AO353_17125 AO353_17125 leucine ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17125 Length = 375 Score = 543 bits (1400), Expect = e-159 Identities = 264/372 (70%), Positives = 312/372 (83%) Query: 1 MKKGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQI 60 M K T+++S+LFAAM +AG AS+S AADTIKI +AGP TGPV QYGDMQ GA MAIEQI Sbjct: 1 MNKATKQISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVTQYGDMQFIGAKMAIEQI 60 Query: 61 NKAGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEG 120 N GGV+G LE YDDACDPKQAVAVANKVVNDGVKFVVGH+CSSSTQPA+DIYEDEG Sbjct: 61 NAKGGVDGKMLEAKEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEG 120 Query: 121 VLMITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEG 180 V+MITP+AT+P+IT+RGYK++FRTIGLD+ QGP AG +IA+ K K +AVLHDKQQYGEG Sbjct: 121 VIMITPAATSPDITNRGYKMVFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEG 180 Query: 181 IATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQA 240 IAT VKKT+E G+KVAVFEGLNAGDKDF+++I KLK+A V FVY+GGYHPE+GL+LRQA Sbjct: 181 IATAVKKTLEGKGVKVAVFEGLNAGDKDFSSIIQKLKQANVDFVYYGGYHPELGLILRQA 240 Query: 241 KQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPS 300 K+ GL+A+FMGPEGVGN I+ IA DASEG+L TLP++F+QDP NKAL+DAF AK QDP+ Sbjct: 241 KEKGLNAKFMGPEGVGNESISQIAQDASEGLLVTLPKSFDQDPANKALVDAFAAKKQDPT 300 Query: 301 GIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTV 360 G FV PAYSAV VIA+GI+ A D KVA A+ A TF+TPTG+L +D KGDLKNF F V Sbjct: 301 GPFVFPAYSAVEVIAEGIKAAKSEDTAKVAAAIHAGTFKTPTGDLSYDAKGDLKNFKFVV 360 Query: 361 YEWHKDATRTEV 372 Y+WH +TEV Sbjct: 361 YQWHFGKPKTEV 372 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: 578 Number of extensions: 16 Number of successful extensions: 1 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: 375 Length adjustment: 30 Effective length of query: 343 Effective length of database: 345 Effective search space: 118335 Effective search space used: 118335 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