Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate 206138 DVU0713 branched-chain amino acid ABC transporter, permease protein
Query= ecocyc::LIVH-MONOMER (308 letters) >MicrobesOnline__882:206138 Length = 301 Score = 264 bits (675), Expect = 2e-75 Identities = 137/301 (45%), Positives = 203/301 (67%), Gaps = 3/301 (0%) Query: 8 FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67 FLQQ+ NG+ +G YALIA+GYTMVYG++ +INFAHG+++ IG+Y+ F + AAL + G Sbjct: 4 FLQQLTNGLAVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGFTVFAALGLSGHV 63 Query: 68 TGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEG 127 +G + V + + + G+ +ERVAYRP+R+S RL A++SA+G SIF QN V L G Sbjct: 64 SGAVAVLLVTTMVMGLVALIGYLLERVAYRPLRSSSRLSAVVSALGASIFFQNAVMLIYG 123 Query: 128 SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRAC 187 ++ P+ V F I ++ +++ + ML L FI +R G A RA Sbjct: 124 AKFQVYPNDIRPTMAVSF---FGMDIPLVRIMMFGASVALMLLLHFFIHRTRTGTAIRAV 180 Query: 188 AEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAAV 247 A D A L+GI+ +RVIAL F+IG A+ AGV++G +YG I+ +G++ G+KAFTAA+ Sbjct: 181 AIDQGAAKLMGIDVNRVIALVFMIGPALGGAAGVMVGLYYGQIDFTMGWVYGLKAFTAAI 240 Query: 248 LGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVEK 307 LGGIG+IPGAM+GGL+LG+ EAL +AY+S +KD ++F +LIL+L++ PTG+LG +K Sbjct: 241 LGGIGNIPGAMVGGLLLGVIEALGAAYISIAWKDAIAFLVLILILIIRPTGLLGERVADK 300 Query: 308 V 308 + Sbjct: 301 I 301 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: 313 Number of extensions: 16 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: 308 Length of database: 301 Length adjustment: 27 Effective length of query: 281 Effective length of database: 274 Effective search space: 76994 Effective search space used: 76994 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 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