Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_011939018.1 GURA_RS10795 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000016745.1:WP_011939018.1 Length = 294 Score = 187 bits (476), Expect = 2e-52 Identities = 108/303 (35%), Positives = 176/303 (58%), Gaps = 19/303 (6%) Query: 9 LQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDT 68 LQ + +G++ G+ YALI +G+ ++Y G+INFA GE M+G +SF + L Sbjct: 8 LQYVLSGLSTGAIYALIGLGFAIIYNSTGIINFAQGEFVMLGGMLSFFFLTTLK------ 61 Query: 69 GWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEGS 128 L + A A+ ++A G + ER+A RP++N+ + +I IG SIF++ L G Sbjct: 62 --LPLFASIPLAVFTSTAAGIAFERLAIRPLKNATPMSLVIITIGASIFIRGLAMLLWGK 119 Query: 129 RDVALPSLFNGQWVVGHSENFSASITTMQAVIWI--VTFLAMLALTIFIRYSRMGRACRA 186 ALPS G+ A T + IWI +T L ++A +F Y+ G+A RA Sbjct: 120 DTHALPSFS------GNDPISVAGATILPQHIWIFAITLLVIIANKLFFYYTISGKAMRA 173 Query: 187 CAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPY-IGFMAGMKAFTA 245 CA + + ASL+GI+ R++ +FVI +A+ ++AG+++ + Y +G M G+K F A Sbjct: 174 CAFNRRAASLVGIDVKRMVLFSFVISSALGSMAGIIIAPL--TMTAYDVGIMLGLKGFCA 231 Query: 246 AVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEV 305 A++GG+ S G +IGGL+LG E+L + +S+ YKD ++F +L+L+L V P G+ + E Sbjct: 232 AIIGGMSSGVGTVIGGLVLGTLESLGAGLISSGYKDAIAFIILLLLLFVRPQGLFKKGET 291 Query: 306 EKV 308 E+V Sbjct: 292 ERV 294 Lambda K H 0.328 0.141 0.410 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: 237 Number of extensions: 11 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: 308 Length of database: 294 Length adjustment: 27 Effective length of query: 281 Effective length of database: 267 Effective search space: 75027 Effective search space used: 75027 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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