Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate Ac3H11_1939 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1939 Length = 291 Score = 160 bits (406), Expect = 2e-44 Identities = 102/300 (34%), Positives = 170/300 (56%), Gaps = 13/300 (4%) Query: 4 FLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGIT 63 F+Q LI+G+S G IYGLIA+G+ ++Y ++FA GE+ M+GAF L +G Sbjct: 3 FVQLLISGVSQGCIYGLIALGFVLIYKATETVSFAQGELMMLGAFCGLALMTVLG----- 57 Query: 64 WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQ- 122 V ++AS++ ++G VER RP+ P + ++ IG+ L+ V ++ Sbjct: 58 ---FPFWVAVLASVVAMGLFGVLVERAVIRPILGQPAFSIVMLTIGIGYVLRGLVTMIPN 114 Query: 123 -GARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACE 181 G + L P+ + +L G + VS +L I T AL + + LG A +A Sbjct: 115 IGTDTHTL-PVPYKDQSLRLGELVVSAEQLVVIGATGALCVLLFAMFRYSKLGIAMQAAS 173 Query: 182 QDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVL 241 Q++ A +G+ V R+ L + + A +AAVAG+++ I + +GF+ G+KAF AAV+ Sbjct: 174 QNQLAAYYMGIPVQRLNGLAWGLAAVVAAVAGLLLAPIT-FVHANMGFI-GLKAFPAAVV 231 Query: 242 GGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEKV 301 GG GSLPGA++GG+VIG++E+ Y+ +KD A + +++++L+ +P GL G +KV Sbjct: 232 GGFGSLPGAIVGGLVIGIVESLSGFYLPDGFKDTAAYIVVLIMLMVKPNGLFGEKLRKKV 291 Lambda K H 0.329 0.144 0.425 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: 302 Number of extensions: 23 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: 301 Length of database: 291 Length adjustment: 26 Effective length of query: 275 Effective length of database: 265 Effective search space: 72875 Effective search space used: 72875 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