Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate Pf1N1B4_3218 High-affinity leucine-specific transport system, periplasmic binding protein LivK (TC 3.A.1.4.1)
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3218 Length = 375 Score = 536 bits (1382), Expect = e-157 Identities = 260/372 (69%), Positives = 314/372 (84%) Query: 1 MKKGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQI 60 M K T+++S+LFAAM +AG AS+S AADTIKI +AGP TGPVAQYGDMQ +G+ MAIEQI Sbjct: 1 MTKATKQISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQI 60 Query: 61 NKAGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEG 120 N GGV+G +LE V YDDACDPKQAVAVANKVVNDGVKFVVGH+CSSSTQPA+DIYEDEG Sbjct: 61 NAKGGVDGKKLEAVEYDDACDPKQAVAVANKVVNDGVKFVVGHLCSSSTQPASDIYEDEG 120 Query: 121 VLMITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEG 180 V+MITP+AT+P+IT+RGYK+IFRTIGLD+ QGP AG +IA+ K K +AVLHDKQQYGEG Sbjct: 121 VIMITPAATSPDITTRGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEG 180 Query: 181 IATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQA 240 IA+ VK T+E G+KVAVFEG+NAGDKDF++++SKLK+A V FVY+GGYHPE+GLLLRQ+ Sbjct: 181 IASAVKTTLEKKGVKVAVFEGINAGDKDFSSMVSKLKQANVDFVYYGGYHPELGLLLRQS 240 Query: 241 KQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPS 300 ++ GL A+FMGPEGVGN I+ IA +ASEG+L TLP++F+QDP N AL DAFKAK +DPS Sbjct: 241 QEKGLKAKFMGPEGVGNDSISQIAKEASEGLLVTLPKSFDQDPANIALADAFKAKKEDPS 300 Query: 301 GIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTV 360 G FV P+YSAV VI +GI+ A D KVAEA+ TF+TPTG+L FDEKGDLK+F F V Sbjct: 301 GPFVFPSYSAVQVIVEGIKAAKSEDTTKVAEAIHKGTFKTPTGDLSFDEKGDLKDFKFVV 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: 553 Number of extensions: 19 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