Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__Miya:8502073 Length = 596 Score = 104 bits (260), Expect = 4e-27 Identities = 78/255 (30%), Positives = 124/255 (48%), Gaps = 21/255 (8%) Query: 14 QLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPLLIQMFL 73 ++L + T+ + S L LL ++ R+S A I FR +PLLIQ+F Sbjct: 56 EILKGLANTVRISLISSALALLLGTMLGLARLSLFRPLRVTATCVIEFFRNTPLLIQLFF 115 Query: 74 VYYGMGQF--GVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAVPVGQIEAG 131 Y+ RE+ ++ + CA + L++ TA + AE+IR GL ++P G +EA Sbjct: 116 WYFAFPAILPDNAREALF--SIQFEFWCATIGLSIYTASFMAEVIRAGLQSIPKGLLEAA 173 Query: 132 YSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQIIQQT 191 YS GLS F +LR +I P+A R +P +E + +K+++LA +V V E+T AQQ+ T Sbjct: 174 YSSGLSYFQVLRTIILPLAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWHAQQVESLT 233 Query: 192 YRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRHLRAARPAAV---------------- 235 ++ E A ++YL L+ +I +L + R+ R V Sbjct: 234 FKGFEATSAATVLYLSLSLIISFILNGVNGRMRLDTAPGRSIPVLVVGALLTPLGLIRRM 293 Query: 236 -SRPVSATTEARRAA 249 RPV+ ARR A Sbjct: 294 FIRPVTRALRARRRA 308 Score = 88.6 bits (218), Expect = 3e-22 Identities = 59/169 (34%), Positives = 89/169 (52%), Gaps = 11/169 (6%) Query: 58 YILVFRGSPLLIQMFLVYYGMG-QFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEII 116 YI + RG+PL+I +F VY+ + FG F W A +L T Y AEI+ Sbjct: 429 YIELIRGNPLIIVIFWVYFFIPVMFGTTLNVF-WS--------ATWALTAFTGAYIAEIV 479 Query: 117 RGGLMAVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVT 176 R G+ +P GQ+EA YS GL+ +RR++ P AL+Q +PA + + + K T+LA ++ Sbjct: 480 RTGIQNIPAGQVEAAYSTGLTYLQAMRRIVLPQALKQMIPAIVGQFIAIFKDTSLAFVLG 539 Query: 177 VWEVTGVAQQIIQQ-TYRTTEVFICAALIYLFLNFVIVRLLGMLETRLS 224 V E+T VAQ I + E++ A +Y + + LE RLS Sbjct: 540 VLELTFVAQGINNRLMIHPMEIYGTVAFLYFICCYSMSVFAARLERRLS 588 Lambda K H 0.331 0.143 0.431 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: 344 Number of extensions: 20 Number of successful extensions: 4 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 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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