Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate 208249 DVU2743 high-affinity branched-chain amino acid ABC ransporter, permease protein
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >MicrobesOnline__882:208249 Length = 306 Score = 211 bits (537), Expect = 2e-59 Identities = 119/308 (38%), Positives = 192/308 (62%), Gaps = 9/308 (2%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVAL-ITFLAIGS 59 ME F+Q + N L G+ Y LIA+GYT+VYG++ +INFAHG+I+M+GA+++ + + +G Sbjct: 1 METFIQNIFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYISFFVASILLGQ 60 Query: 60 LGITWV---PLALLVMLVASMLFTAVYGWTVERIAYRPLR--SSPRLAPLISAIGMSIFL 114 +G + P+AL + + +M+ TA G T+ER+AYRPLR + RL +I+A+ I L Sbjct: 61 IGGFFELSGPMALALTVPLTMVLTAGVGVTLERVAYRPLRRKGAHRLYVVITALMCGIML 120 Query: 115 QNYVQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQ-LITRTSL 173 +N L GA K L P + + G VSV+ ++L +++T L++ Q ++TRT + Sbjct: 121 ENGNLALLGASRKAL-PEMIDKVVYTIGTVSVTNLKLM-VIVTAFLVFALLQFIVTRTRI 178 Query: 174 GRAQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGV 233 G A RA DK L+G+ +D +I TFV+G+ A +AG++ + Y ++D Y+G + G Sbjct: 179 GMAMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGW 238 Query: 234 KAFTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLL 293 KAF AAV+GGIG + GA +GG ++ IE + S ++D+ F+IL+ ++ RPTGL Sbjct: 239 KAFIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAVFPSTFRDLFAFSILLFIMWQRPTGLF 298 Query: 294 GRPEIEKV 301 G + K+ Sbjct: 299 GVAKTTKI 306 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: 277 Number of extensions: 17 Number of successful extensions: 3 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: 306 Length adjustment: 27 Effective length of query: 274 Effective length of database: 279 Effective search space: 76446 Effective search space used: 76446 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