Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= uniprot:A0A0H3PA28 (219 letters) >MicrobesOnline__882:206177 Length = 596 Score = 125 bits (315), Expect = 1e-33 Identities = 72/204 (35%), Positives = 115/204 (56%), Gaps = 5/204 (2%) Query: 6 NAQNIEFLMQ--GLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNT 63 N Q+ E M GL +L +A+ +S G + I + +R+ + YI++ R Sbjct: 377 NGQSDELFMGLGGLAYSLLMAVIAISVSFFIGLVVGIGRTSDNRICRIPCLLYIELIRGN 436 Query: 64 PLLLWMLAACFVLPVFFGQFPQAFWG-TIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYS 122 PL++ + F +PV F F FW TI +L+T + +AEI+R G+ +IP GQ EAAYS Sbjct: 437 PLIIVIFWIYFFIPVLFNTFFNVFWSATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYS 496 Query: 123 QGFGKFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTS 182 G T+ IILPQ +++IPA++ Q + KDT+ LG+ ELT+ ++ I +L Sbjct: 497 TGLTFVQTMRRIILPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLELTFVAQGINNRLMV 556 Query: 183 FEEILAMIGVVAGIYFIICFSLSM 206 + + + G VA +YFI C+S+S+ Sbjct: 557 YP--MEIYGTVAFLYFICCWSMSV 578 Score = 115 bits (288), Expect = 2e-30 Identities = 76/205 (37%), Positives = 113/205 (55%), Gaps = 14/205 (6%) Query: 13 LMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLL----W 68 +++GL +T++I+L + +++ GT L I + + A ++ FRNTPLL+ W Sbjct: 57 ILKGLGVTVRISLISSALALGLGTVLGIARLSLFAPLRLTATAVVEFFRNTPLLVQLFFW 116 Query: 69 MLAACFVLP------VFFGQFPQAFW-GTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAY 121 A +LP +F G F FW TIG S+YTS+ MAE+IR GL SIPKG EAAY Sbjct: 117 YFAFPAILPENIRELLFTGNFE--FWCATIGLSVYTSAFMAEVIRAGLQSIPKGLLEAAY 174 Query: 122 SQGFGKFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILA-KL 180 S G L IILP FR IIP L S+ + +K+++ +G+AELT+ S+ + + Sbjct: 175 SSGLNYVQVLRTIILPMAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWQSQQVESLTF 234 Query: 181 TSFEEILAMIGVVAGIYFIICFSLS 205 FE A + + +I F L+ Sbjct: 235 KGFEATSAATVLYLSLSLLISFILN 259 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: 407 Number of extensions: 29 Number of successful extensions: 6 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