Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate Dsui_0629 Dsui_0629 branched-chain amino acid ABC-type transport system, permease component
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__PS:Dsui_0629 Length = 307 Score = 398 bits (1023), Expect = e-116 Identities = 196/309 (63%), Positives = 254/309 (82%), Gaps = 2/309 (0%) Query: 1 MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQV 60 MDIF+QQIINGLVLGS+YAL+ALGYTMVYG+L LINFAHG+++M+GA+ L+++K++ Sbjct: 1 MDIFLQQIINGLVLGSIYALVALGYTMVYGILGLINFAHGEVVMIGALTALTVVKLL--A 58 Query: 61 APGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAM 120 GLPG V +I ++ A PVC+ + IE+IAYRPLR APRLAPLITAIGVSI+LQ LAM Sbjct: 59 GSGLPGPVIALIGLMAAAPVCMAIGYGIEKIAYRPLRKAPRLAPLITAIGVSIVLQNLAM 118 Query: 121 MIWGRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRAT 180 M+WGRS FP V+P++ + GA + Q++++ +A M GL+L++ +T++GRAMRAT Sbjct: 119 MVWGRSYHSFPAVLPAEAHEVLGATFTDLQVIIVLVAAGMMAGLLLLINRTRLGRAMRAT 178 Query: 181 AENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAV 240 AENP IA LMGV+ N +I +TF IG+ LAA+AG+M +ANYS A + MGF+ GLKAF+AAV Sbjct: 179 AENPAIAQLMGVNVNHIISLTFVIGSALAAVAGLMVSANYSIAHYYMGFILGLKAFTAAV 238 Query: 241 LGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGI 300 LGGIGN+ GAM+GGILLGLIESLGAGYIGD+TG FLGS+YQD+FAF VLI+VL RPSG+ Sbjct: 239 LGGIGNLAGAMIGGILLGLIESLGAGYIGDITGGFLGSHYQDVFAFFVLILVLVFRPSGL 298 Query: 301 MGERVADRA 309 +GE+VA+RA Sbjct: 299 VGEKVAERA 307 Lambda K H 0.328 0.144 0.416 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: 361 Number of extensions: 13 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: 309 Length of database: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 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 (21.7 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