Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_013010203.1 DACET_RS04490 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000025725.1:WP_013010203.1 Length = 300 Score = 301 bits (771), Expect = 1e-86 Identities = 154/302 (50%), Positives = 216/302 (71%), Gaps = 4/302 (1%) Query: 7 YFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI 66 YFL+ G+T GS YALIA+GYTMVYGII +INFAHGE+YMIG++ + + + ++G Sbjct: 3 YFLELFLGGLTRGSIYALIALGYTMVYGIIQLINFAHGEIYMIGAFTALIFASVFSILGW 62 Query: 67 DTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTE 126 + + A + A+V +SAYG++IE++AY+P+RN+ RL LISAIGMS+FLQNYV L + Sbjct: 63 PVAAIFIIAT-LAAVVYSSAYGYTIEKIAYKPLRNAPRLSPLISAIGMSLFLQNYVLLAQ 121 Query: 127 GSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRA 186 S + P L E S ++ + I T + ML LT FI+++ MG+A RA Sbjct: 122 TSDFLPFPQLIPD---FEFMEPISHIFSSAELAIVSTTIIVMLLLTFFIKFTNMGKAMRA 178 Query: 187 CAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAA 246 A+D MA L+GIN DRVI++TF+IG+A+AA+ GVL+ G +N YIGF+AG+KAFTAA Sbjct: 179 TAQDKTMALLIGINVDRVISVTFIIGSALAALGGVLIANHIGQVNFYIGFIAGIKAFTAA 238 Query: 247 VLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVE 306 VLGGIGSIPGA++G LILG E+ ++ Y+S++Y+DV +FALL+L+L+ P G+LGR E + Sbjct: 239 VLGGIGSIPGAVLGALILGWTESFATGYISSDYEDVFAFALLVLILIFRPAGLLGRSETK 298 Query: 307 KV 308 KV Sbjct: 299 KV 300 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: 295 Number of extensions: 11 Number of successful extensions: 4 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: 300 Length adjustment: 27 Effective length of query: 281 Effective length of database: 273 Effective search space: 76713 Effective search space used: 76713 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