Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3784 Psest_3853 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__psRCH2:GFF3784 Length = 266 Score = 140 bits (353), Expect = 3e-38 Identities = 95/281 (33%), Positives = 147/281 (52%), Gaps = 31/281 (11%) Query: 3 SPVTNTMSDDT-LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCIT 61 +P N D T +L L +FGG +A+N+ + + + ALIGPNGAGKTTVFN +T Sbjct: 9 NPTGNAGRDATVMLSARGLRKEFGGFVAVNNVDLDVRHAQVHALIGPNGAGKTTVFNLLT 68 Query: 62 GFYKPTMGMITFNQKSGKQYLLERLPDFRITK--EARVA-----RTFQNIRLFSGLTVLE 114 F +P+ G I RL D IT+ A+VA R+FQ +F LTVL+ Sbjct: 69 KFLQPSAGSI-------------RLLDHDITRTDPAKVARMGLVRSFQISAVFPHLTVLD 115 Query: 115 NLLVAQHNKLMKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPY 174 N+ VA L + G + + R A++L +E L D+ + A DL Y Sbjct: 116 NVRVA----LQRPGGLATQFWLPMRSLNRLNERALQL----IESVGLADKRHELAADLSY 167 Query: 175 GAQRRLEIARAMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSV 234 G +R LEIA + P++L LDEP AG+ + + +++ + T ++L++EH++ V Sbjct: 168 GRKRVLEIATTLALEPKVLLLDEPMAGMGHEDVHVVAEIIREV--ATQRAVLMVEHNLKV 225 Query: 235 VMEISDHVVVLEYGQKISDGTPDHVKNDPRVIAAYLGVEDE 275 V ++ V VL+ G+ ++ G V D RV AY+G +D+ Sbjct: 226 VADLCHQVTVLQRGEILTSGDYRTVSQDERVRVAYMGTDDD 266 Lambda K H 0.318 0.136 0.386 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: 182 Number of extensions: 12 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: 292 Length of database: 266 Length adjustment: 26 Effective length of query: 266 Effective length of database: 240 Effective search space: 63840 Effective search space used: 63840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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