Align arginine/ornithine transport protein (characterized)
to candidate HSERO_RS11445 HSERO_RS11445 ABC transporter permease
Query= CharProtDB::CH_107317 (229 letters) >FitnessBrowser__HerbieS:HSERO_RS11445 Length = 221 Score = 121 bits (303), Expect = 1e-32 Identities = 76/213 (35%), Positives = 121/213 (56%), Gaps = 15/213 (7%) Query: 8 TIVDGAWLTLQLALLSMLLAIVLGLLGAAFRLSPVRWLAW--CGDLYATVVRGIPDLVLI 65 ++V G +T+++ S+++ VLGLL RLSP R + + C +Y T+VRG P LV + Sbjct: 14 SLVHGTLVTVEITAASLVVGCVLGLLVGLGRLSPQRRVIYGLC-TIYLTLVRGTPLLVQL 72 Query: 66 LLIFYGGQGLLNWVAPQLGYDDYIDLNPFVSGVGTLGFIFGAYLSETFRGAFMAIPKGQG 125 L F+G P +G + L +V G+ LG GAY+SE RGA +I +GQ Sbjct: 73 FLWFFG--------LPHVG----VILPAYVCGILGLGIYSGAYVSEIVRGAIQSIERGQM 120 Query: 126 EAGYGYGMSHRQVFFRIQVPQMIRLAIPGFTNNWLVLVKATALISVVGLQDMMFKAKQAS 185 EA G+ +R R+ +PQ IP N ++ L+K +AL+S++ + D+M + ++ Sbjct: 121 EAARSLGLPYRMAMRRVILPQAFVRMIPPLGNEFIALIKNSALVSLLTIADLMHEGEKII 180 Query: 186 DATREPFTYYLAVAGLYLLVTSVSLLLLRLLER 218 T YLA+A +YLL+TSV+ L+LR +E+ Sbjct: 181 SVTYRSLETYLAIALIYLLLTSVTTLILRRVEK 213 Lambda K H 0.328 0.144 0.442 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: 94 Number of extensions: 3 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: 229 Length of database: 221 Length adjustment: 22 Effective length of query: 207 Effective length of database: 199 Effective search space: 41193 Effective search space used: 41193 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: 46 (22.3 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