Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate HSERO_RS08270 HSERO_RS08270 amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__HerbieS:HSERO_RS08270 Length = 373 Score = 462 bits (1190), Expect = e-135 Identities = 225/374 (60%), Positives = 292/374 (78%), Gaps = 5/374 (1%) Query: 3 KGTQRLSRLFAAMAIAGFASYSMAA--DTIKIALAGPVTGPVAQYGDMQRAGALMAIEQI 60 K RL+++ A+A A FA+++ A +T+KIA+AGP+TG VAQYGDM +AGAL AIEQI Sbjct: 2 KFASRLTKI--ALAAATFAAFAGVAHAETVKIAIAGPMTGAVAQYGDMVKAGALTAIEQI 59 Query: 61 NKAGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEG 120 N AGG NG + E V+ DDAC+PKQAVAVANK+V+ G+K+V+GHVCS ST PA+DIYE+EG Sbjct: 60 NAAGGANGNKFEAVMMDDACEPKQAVAVANKIVSQGIKYVIGHVCSGSTIPASDIYENEG 119 Query: 121 VLMITPSATAPEIT-SRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGE 179 V+MITPSATAP++T ++ +K IFRTIG D+ QGP A +++ E+ K K +AVLHDKQ YG+ Sbjct: 120 VVMITPSATAPQLTEAKPHKFIFRTIGRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQ 179 Query: 180 GIATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQ 239 G+A+ VK ++ A + V VFEG+NAGD D++A+++KLK GV FVYFGGYHPEMGL++RQ Sbjct: 180 GVASSVKAALDAAKVPVVVFEGINAGDSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQ 239 Query: 240 AKQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDP 299 A++ G+ A FMGPEGVGN +ITAIAG ASEGML TLP F DP N AL+ AF A +DP Sbjct: 240 AREQGIKAVFMGPEGVGNKDITAIAGPASEGMLVTLPADFAADPANAALVKAFAAAKRDP 299 Query: 300 SGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFT 359 +G F +PAYS V +IA I A DPEKVA + AN+F+TP GN+ +D+KGDLK+F F Sbjct: 300 NGPFQMPAYSGVKIIADAIAGAKSTDPEKVAAYIHANSFKTPIGNVEYDKKGDLKSFKFV 359 Query: 360 VYEWHKDATRTEVK 373 V+ WHKDA++TE K Sbjct: 360 VFTWHKDASKTEAK 373 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: 506 Number of extensions: 23 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: 373 Length of database: 373 Length adjustment: 30 Effective length of query: 343 Effective length of database: 343 Effective search space: 117649 Effective search space used: 117649 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