Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate RR42_RS14425 RR42_RS14425 leucine ABC transporter substrate-binding protein
Query= uniprot:A0A160A0J6 (375 letters) >FitnessBrowser__Cup4G11:RR42_RS14425 Length = 371 Score = 427 bits (1098), Expect = e-124 Identities = 217/374 (58%), Positives = 268/374 (71%), Gaps = 4/374 (1%) Query: 1 MTKATKQISKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQI 60 MT + L A+ G A++ A+TIKI IAGP +G VAQYGDM +G+ AIEQI Sbjct: 1 MTLSRLTSISLATALCALGAAAN---AETIKIAIAGPMSGSVAQYGDMVKAGALTAIEQI 57 Query: 61 NAKGGVNGKQLVAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEG 120 NA GG G + V DDAC+PKQAVAVANK+V+ I +V+GH+CS ST PASDIYE+EG Sbjct: 58 NAAGGAGGNKFEVVMMDDACEPKQAVAVANKIVSQKIHYVIGHVCSGSTIPASDIYENEG 117 Query: 121 VVMITPAATSPDITA-RGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGE 179 +VM+TP+AT+P +T + K IFRTIG D QGPAA YI +KPK VA+LHDKQ YG+ Sbjct: 118 IVMVTPSATAPQLTENKKRKFIFRTIGRDDQQGPAAAQYIITKIKPKKVAILHDKQSYGQ 177 Query: 180 GIASAVKKTLEDKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQ 239 GIAS+VKK LE + VAVFEGVNAGD D+S++I KLK VDFVY+GGYHPE+GL+LRQ Sbjct: 178 GIASSVKKDLEAAKIPVAVFEGVNAGDSDYSAVITKLKSQGVDFVYFGGYHPEMGLLLRQ 237 Query: 240 SQEKGLKAKFMGPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDP 299 ++E+G+KA FMGPEGVGN ++ IA SSEG+LVTLP F DP+N AL AF KK D Sbjct: 238 AREQGVKATFMGPEGVGNKDVTAIAGASSEGMLVTLPADFSADPSNAALVKAFADKKRDA 297 Query: 300 SGPFVFPSYSAVTVIADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFV 359 +GPF P+Y+AV +I DAI AKS D KVA +H F+TP G + +D GDLK FKFV Sbjct: 298 NGPFQMPAYAAVQIIGDAIAGAKSTDPTKVAAYMHKNAFQTPIGKVEYDAQGDLKSFKFV 357 Query: 360 VYEWHFGKPKTEAS 373 V+ WH KT A+ Sbjct: 358 VFTWHKDATKTAAN 371 Lambda K H 0.314 0.132 0.372 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: 484 Number of extensions: 25 Number of successful extensions: 2 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: 375 Length of database: 371 Length adjustment: 30 Effective length of query: 345 Effective length of database: 341 Effective search space: 117645 Effective search space used: 117645 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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