Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate SMa2197 SMa2197 ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__Smeli:SMa2197 Length = 304 Score = 98.2 bits (243), Expect = 3e-25 Identities = 50/128 (39%), Positives = 82/128 (64%), Gaps = 4/128 (3%) Query: 246 TALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVPS 305 TA +LGL GA+++EIIR G++SV GQ +AA +LG+T +TLW+I++PQA+ VI+P Sbjct: 158 TAAVLGLGLNEGAYMSEIIRSGLMSVDPGQRQAAKSLGMTNGKTLWRILLPQAMPVIIPP 217 Query: 306 LNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGMN 365 +Q +G K SSL + DL +AQT ++ + + + ++ + YLA ++SA Sbjct: 218 TGNQTIGMLKTSSLVSVISLADLLYSAQTIYSRNFQTIPLLIVACIWYLAATTILSA--- 274 Query: 366 GLQQRLQR 373 +Q R++R Sbjct: 275 -VQVRIER 281 Score = 44.3 bits (103), Expect = 4e-09 Identities = 22/79 (27%), Positives = 44/79 (55%), Gaps = 3/79 (3%) Query: 64 NIGESAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSR 123 N G +A DS ++ GL ++ + + +++ V+GT+ + A ++N ++ ++ Sbjct: 51 NFGWDVVADYLFDS---RILWGLSLTVWLTVVTMVIGVVLGTIFAIMAMADNVVISTVAN 107 Query: 124 GYVAVVRNTPLLLQLIVWY 142 Y+ R TP+L+QLI WY Sbjct: 108 AYIWFFRGTPVLVQLIFWY 126 Lambda K H 0.326 0.140 0.445 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: 268 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 304 Length adjustment: 28 Effective length of query: 349 Effective length of database: 276 Effective search space: 96324 Effective search space used: 96324 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: 49 (23.5 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