Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate RR42_RS02580 RR42_RS02580 amino acid ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__Cup4G11:RR42_RS02580 Length = 242 Score = 92.4 bits (228), Expect = 1e-23 Identities = 73/231 (31%), Positives = 112/231 (48%), Gaps = 19/231 (8%) Query: 156 WHWLGSLYLSKQG-IYLPWPQTPGWLVVILA-----IALVLFVSWLAQRQRSPRDWRWLY 209 WHW L + Q YL W + + + L IALV+ S L + P +WL Sbjct: 5 WHWGVFLEQAAQNETYLDWMISGLKVTIALGLSSWIIALVIG-SVLGVLRTVPN--KWLS 61 Query: 210 GAIAVVTVLM----LLTQLSWPQQLQPGQIRGGLRL------SLEFTALLLGLVAYTGAF 259 G A + LL QL + P + GG + +F A +L L +T A Sbjct: 62 GLAATYVEIFRNIPLLVQLFIWYFVMPELLPGGESFKQMNPFAQQFLAAMLCLGTFTAAR 121 Query: 260 ITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSL 319 + E +R GI S+P GQ A A+G T +QT +++P + RVIVP L S+++ KNS++ Sbjct: 122 VCEQVRSGINSLPPGQRNAGLAMGFTLAQTYRYVLLPMSFRVIVPPLTSEFLNIFKNSAV 181 Query: 320 AIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGMNGLQQR 370 A +G +L A + ++ T RP E F+ + + Y IN V+ M ++ R Sbjct: 182 ASTIGLLELAAQGRQLVDYTARPYESFIAVTIMYALINIVVMLLMRWVEGR 232 Score = 48.9 bits (115), Expect = 1e-10 Identities = 29/72 (40%), Positives = 43/72 (59%), Gaps = 4/72 (5%) Query: 86 LVNSLRV-IAIGL---ILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVW 141 +++ L+V IA+GL I+ VIG++ GV N L L+ YV + RN PLL+QL +W Sbjct: 24 MISGLKVTIALGLSSWIIALVIGSVLGVLRTVPNKWLSGLAATYVEIFRNIPLLVQLFIW 83 Query: 142 YFPILLSLPAAQ 153 YF + LP + Sbjct: 84 YFVMPELLPGGE 95 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: 253 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 242 Length adjustment: 27 Effective length of query: 350 Effective length of database: 215 Effective search space: 75250 Effective search space used: 75250 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