Align Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale)
to candidate WP_068463508.1 APY04_RS13100 urea ABC transporter permease subunit UrtB
Query= uniprot:A0A0D9B2B6 (307 letters) >NCBI__GCF_001541235.1:WP_068463508.1 Length = 291 Score = 126 bits (316), Expect = 7e-34 Identities = 91/301 (30%), Positives = 153/301 (50%), Gaps = 24/301 (7%) Query: 11 LVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLDSVPL 70 L+ G+++ S + + A+G T++YG G+IN AHG + M+G+Y +++ + + L +P Sbjct: 10 LILGVSIASIWLIAALGLTIIYGAAGVINMAHGALIMLGAYSSYMLQHYIGVPYLLCIP- 68 Query: 71 LMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLL--SQDSK 128 AS V+ S G +ER + L L L++ G+S+ L V L D K Sbjct: 69 -------ASFVIVSIIGLILERGLIQYLY-DRPLDTLLATYGVSLVLVQGVRLIFGSDPK 120 Query: 129 DKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRACAE 188 ++P + N ++G IS ++VV VT + +L L + ++R G RA + Sbjct: 121 YLAVPEIFSSNISLGFAN-----ISTFRVVVIAVTALLVLALWILFYKTRFGIQVRAVMQ 175 Query: 189 DIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVIN---PNAGFLVGLKAFTAA 245 + +MA GIN++ I +TF +GA LA +A L +GV+N P G ++AF Sbjct: 176 NKEMAASFGINSSRIYMMTFALGAGLAGVAGSL----FGVLNIVLPTMGDSYVVQAFLMV 231 Query: 246 VLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRPEVE 305 V GG G++ G ++ G ++ A I D + V F L+V+ L FRP G+ + V Sbjct: 232 VAGG-GTLAGTVIASAFTGELQSVFAFITNDTFARFVIFLLIVVFLRFRPQGLFAKGGVR 290 Query: 306 K 306 + Sbjct: 291 R 291 Lambda K H 0.327 0.144 0.411 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: 244 Number of extensions: 17 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: 307 Length of database: 291 Length adjustment: 27 Effective length of query: 280 Effective length of database: 264 Effective search space: 73920 Effective search space used: 73920 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 (21.7 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