Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate 209487 DVU0548 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= ecocyc::LIVH-MONOMER (308 letters) >MicrobesOnline__882:209487 Length = 302 Score = 310 bits (793), Expect = 4e-89 Identities = 156/302 (51%), Positives = 224/302 (74%), Gaps = 4/302 (1%) Query: 7 YFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI 66 YF + +F G+T GS YALIA+GYTMVYGII +INFAHGEVYMIG++ + ++ L + G Sbjct: 5 YFCELLFGGLTRGSIYALIALGYTMVYGIIELINFAHGEVYMIGAFTALIVAGVLGIYGF 64 Query: 67 DTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTE 126 +L+ A V A++ +AYG+++E+VAY+P+R++ RL LISAIGMSIFLQNYV L + Sbjct: 65 PEAGILIIAAIV-AVIYCAAYGFTLEKVAYKPLRDAPRLSPLISAIGMSIFLQNYVILAQ 123 Query: 127 GSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRA 186 S V P L ++ E + T +I + + + M+ LT+FI+Y+RMG+A RA Sbjct: 124 TSDFVPFPRLVPDLAIL---EPIAHITGTSDVLIIVTSAITMVGLTLFIKYTRMGKAMRA 180 Query: 187 CAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAA 246 A++ KMA LLGI+ DRVI+LTF+IG+++AA+ GVL+ G +N IGF+AG+KAFTAA Sbjct: 181 TAQNRKMAMLLGIDADRVISLTFIIGSSLAAIGGVLIASHIGQVNFAIGFIAGIKAFTAA 240 Query: 247 VLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVE 306 VLGGIGSIPGAM GGL+LG+ E+ ++ Y+S++Y+D ++FALL+L+L+ P+GILG+P+ + Sbjct: 241 VLGGIGSIPGAMAGGLVLGLCESFATGYVSSDYEDALAFALLVLILIFRPSGILGKPKTQ 300 Query: 307 KV 308 KV Sbjct: 301 KV 302 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: 308 Number of extensions: 16 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: 302 Length adjustment: 27 Effective length of query: 281 Effective length of database: 275 Effective search space: 77275 Effective search space used: 77275 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