Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::A1VZQ3 (250 letters) >FitnessBrowser__Miya:8502073 Length = 596 Score = 128 bits (322), Expect = 2e-34 Identities = 74/230 (32%), Positives = 128/230 (55%), Gaps = 6/230 (2%) Query: 18 WGLYDENSISPFAVWKFLDAL-DNKDAFINGFIYTLEVSILALLIATIFGTIGGVMATSR 76 W + EN + +W F D + G Y+L ++++A+ ++ G GV +S Sbjct: 360 WHVVFEN-LRSLLIWHFPTGRPDEMFLGLGGLAYSLLMAVIAISVSFFIGLAVGVGRSSS 418 Query: 77 FKIIRAYTRIYVELFQNVPLVIQIFFLFYALPVL-GIRLDIFTIGVLGVGAYHGAYVSEV 135 ++ R +Y+EL + PL+I IF++++ +PV+ G L++F + A+ GAY++E+ Sbjct: 419 NRVFRIPCLLYIELIRGNPLIIVIFWVYFFIPVMFGTTLNVFWSATWALTAFTGAYIAEI 478 Query: 136 VRSGILAVPRGQFEASASQGFTYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIV 195 VR+GI +P GQ EA+ S G TY+Q MR I++PQ ++ ++P + Q + + K+TS+ ++ Sbjct: 479 VRTGIQNIPAGQVEAAYSTGLTYLQAMRRIVLPQALKQMIPAIVGQFIAIFKDTSLAFVL 538 Query: 196 GGAELMHSADSYAADYGNYAPAYIFAAV--LYFIICYPLAYFAKAYENKL 243 G EL A + P I+ V LYFI CY ++ FA E +L Sbjct: 539 GVLELTFVAQGINNRLMIH-PMEIYGTVAFLYFICCYSMSVFAARLERRL 587 Score = 115 bits (289), Expect = 2e-30 Identities = 61/209 (29%), Positives = 116/209 (55%), Gaps = 9/209 (4%) Query: 45 INGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLF 104 + G T+ +S+++ +A + GT+ G+ S F+ +R +E F+N PL+IQ+FF + Sbjct: 58 LKGLANTVRISLISSALALLLGTMLGLARLSLFRPLRVTATCVIEFFRNTPLLIQLFFWY 117 Query: 105 YALPVL---GIRLDIFTI------GVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQG 155 +A P + R +F+I +G+ Y ++++EV+R+G+ ++P+G EA+ S G Sbjct: 118 FAFPAILPDNAREALFSIQFEFWCATIGLSIYTASFMAEVIRAGLQSIPKGLLEAAYSSG 177 Query: 156 FTYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYA 215 +Y Q +R II+P R I+PP+ ++ +N +KN+S+ ++VG AEL A + Sbjct: 178 LSYFQVLRTIILPLAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWHAQQVESLTFKGF 237 Query: 216 PAYIFAAVLYFIICYPLAYFAKAYENKLK 244 A A VLY + +++ +++ Sbjct: 238 EATSAATVLYLSLSLIISFILNGVNGRMR 266 Lambda K H 0.328 0.143 0.422 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: 378 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: 250 Length of database: 596 Length adjustment: 30 Effective length of query: 220 Effective length of database: 566 Effective search space: 124520 Effective search space used: 124520 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 (21.8 bits) S2: 50 (23.9 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