Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate WP_008511689.1 BIBO1_RS19985 amino acid ABC transporter permease
Query= uniprot:A0A0H3PA28 (219 letters) >NCBI__GCF_000182725.1:WP_008511689.1 Length = 323 Score = 95.1 bits (235), Expect = 1e-24 Identities = 73/217 (33%), Positives = 109/217 (50%), Gaps = 14/217 (6%) Query: 5 FNAQNIEFLM-QGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNT 63 F A+ I FL+ QG TL I+ + I+ + AI K + + L+ Y +FR Sbjct: 109 FIARKISFLITQGTVTTLYISAISIAIATIIALIGAIAKLSQNGVIYGLSTFYTSLFRGL 168 Query: 64 PLLLWMLAACFVLPVF---FGQFPQAFWGTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAA 120 PLL+ + LP G P G + SL + M EI R G+ SIP GQ EAA Sbjct: 169 PLLMQIYIIYLGLPQIGYVIGAIPA---GILALSLCYGAYMTEIFRAGIESIPHGQKEAA 225 Query: 121 YSQGFGKFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKL 180 + G G T++ +ILPQ R IIP +Q + +KD++ ++ +G+ EL Y ++T Sbjct: 226 TALGLGSAQTMWLVILPQAMRIIIPPTGNQFIAMLKDSSLVSVIGVWELMYVART--QGQ 283 Query: 181 TSFEEILAMIGVVAGIYFIICFSL----SMLVRYYAK 213 T F I M+ + IY+I+ S S + RYYA+ Sbjct: 284 TEFRHI-EMLITASMIYWILSISFEFIQSRIERYYAR 319 Lambda K H 0.331 0.144 0.428 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: 201 Number of extensions: 11 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: 219 Length of database: 323 Length adjustment: 25 Effective length of query: 194 Effective length of database: 298 Effective search space: 57812 Effective search space used: 57812 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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