Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= uniprot:A0A0H3PA28 (219 letters) >FitnessBrowser__Miya:8502073 Length = 596 Score = 122 bits (305), Expect = 2e-32 Identities = 79/205 (38%), Positives = 117/205 (57%), Gaps = 14/205 (6%) Query: 13 LMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLL----W 68 +++GL T++I+L + ++++ GT L + + R + A C I+ FRNTPLL+ W Sbjct: 57 ILKGLANTVRISLISSALALLLGTMLGLARLSLFRPLRVTATCVIEFFRNTPLLIQLFFW 116 Query: 69 MLAACFVLP------VFFGQFPQAFW-GTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAY 121 A +LP +F QF FW TIG S+YT+S MAE+IR GL SIPKG EAAY Sbjct: 117 YFAFPAILPDNAREALFSIQFE--FWCATIGLSIYTASFMAEVIRAGLQSIPKGLLEAAY 174 Query: 122 SQGFGKFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILA-KL 180 S G F L IILP FR IIP L S+ + +K+++ +G+AELT++++ + + Sbjct: 175 SSGLSYFQVLRTIILPLAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWHAQQVESLTF 234 Query: 181 TSFEEILAMIGVVAGIYFIICFSLS 205 FE A + + II F L+ Sbjct: 235 KGFEATSAATVLYLSLSLIISFILN 259 Score = 115 bits (288), Expect = 2e-30 Identities = 63/192 (32%), Positives = 107/192 (55%), Gaps = 3/192 (1%) Query: 16 GLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLLWMLAACFV 75 GL +L +A+ +S G + + ++ +R+ + YI++ R PL++ + F Sbjct: 389 GLAYSLLMAVIAISVSFFIGLAVGVGRSSSNRVFRIPCLLYIELIRGNPLIIVIFWVYFF 448 Query: 76 LPVFFGQFPQAFWG-TIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYSQGFGKFFTLFYI 134 +PV FG FW T + +T + +AEI+R G+ +IP GQ EAAYS G + I Sbjct: 449 IPVMFGTTLNVFWSATWALTAFTGAYIAEIVRTGIQNIPAGQVEAAYSTGLTYLQAMRRI 508 Query: 135 ILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTSFEEILAMIGVVA 194 +LPQ +++IPA++ Q + KDT+ LG+ ELT+ ++ I +L + + G VA Sbjct: 509 VLPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLELTFVAQGINNRLMIHP--MEIYGTVA 566 Query: 195 GIYFIICFSLSM 206 +YFI C+S+S+ Sbjct: 567 FLYFICCYSMSV 578 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: 386 Number of extensions: 21 Number of successful extensions: 5 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: 219 Length of database: 596 Length adjustment: 29 Effective length of query: 190 Effective length of database: 567 Effective search space: 107730 Effective search space used: 107730 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: 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