Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_011188509.1 DP_RS06410 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU0 (300 letters) >NCBI__GCF_000025945.1:WP_011188509.1 Length = 296 Score = 140 bits (354), Expect = 3e-38 Identities = 91/301 (30%), Positives = 160/301 (53%), Gaps = 27/301 (8%) Query: 2 EYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIF 61 + FVQ LL G+T GS+Y +VAIG+ ++Y G+INFA G+ MLGG ++ + F Sbjct: 4 QLFVQYLLAGITYGSMYAIVAIGFNIIYNTTGIINFAQGEFVMLGGMLSISLLQ-----F 58 Query: 62 AGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQV 121 LP+A+ L V+L +A+ +E + R L+ L ++ +G+SI L Sbjct: 59 MPLPLAIGLAVVLTMAV------GGLVEILFIRWLKNPGVLRMIVITVGLSILLREIALH 112 Query: 122 TQGPRNKPIPPMVSSVYQFGN-ISVSL-------KQIIIIVITAVLLTIFWYIVNRTA-L 172 G +P Y +GN IS + QI+ ++ +LL + ++ +T+ + Sbjct: 113 IWGEGVYSLP------YFYGNEISTVVILGARVSPQILWVIGVCLLLVVLLHLFFKTSPM 166 Query: 173 GRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGV 232 GR RA ++K A L G+N ++ +F++ A + A+AG + + ++ G + Sbjct: 167 GREMRACAVNKKAALLCGINARNMVTFSFMLSAGIGALAGAV-MSPITYTQYDSGAALAI 225 Query: 233 KAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGIL 292 K FT A+LGG+G+L GAV G+L+G++E+ + +A++D ++L +L +P G+ Sbjct: 226 KGFTVAILGGLGNLFGAVAAGILLGVLEAFSVSVLPLAFQDAIAISLLLVILCVRPHGLF 285 Query: 293 G 293 G Sbjct: 286 G 286 Lambda K H 0.329 0.143 0.421 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: 265 Number of extensions: 14 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: 300 Length of database: 296 Length adjustment: 26 Effective length of query: 274 Effective length of database: 270 Effective search space: 73980 Effective search space used: 73980 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 24 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