Align Facilitated trehalose transporter Tret1; AmTRET1 (characterized)
to candidate 16922 b2841 arabinose transporter (NCBI)
Query= SwissProt::A9ZSY2 (502 letters) >FitnessBrowser__Keio:16922 Length = 472 Score = 215 bits (547), Expect = 3e-60 Identities = 135/451 (29%), Positives = 237/451 (52%), Gaps = 21/451 (4%) Query: 41 MQLLAALAVSMASLMIGYSSSYTSPALVSMRDNTTATFEVTMDMAMWIGSIMPLSALIGG 100 M + ++A ++A L+ G + AL + D+ F +T + W+ S M L A IG Sbjct: 21 MNMFVSVAAAVAGLLFGLDIGVIAGALPFITDH----FVLTSRLQEWVVSSMMLGAAIGA 76 Query: 101 IIGGPCIEYIGRRNTILSTALPFLAGWLFIALATNVAMILVGRSICGFCVGVASLSLPVY 160 + G +GR+ ++++ A+ F+ G + A AT+V M++ R + G VG+AS + P+Y Sbjct: 77 LFNGWLSFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARVVLGIAVGIASYTAPLY 136 Query: 161 LGESIQPEVRGSLGLLPTVFGNSGILMCF---TAGMYLA-WRNLALLGACIPIIFLILMF 216 L E VRG + + + GI++ F TA Y WR + + A ++ +IL+ Sbjct: 137 LSEMASENVRGKMISMYQLMVTLGIVLAFLSDTAFSYSGNWRAMLGVLALPAVLLIILVV 196 Query: 217 LIPETPRWYISKGKIKEARKSLQWLRGKTADISEELDSIQKMHIESERIATEGALIELFR 276 +P +PRW KG+ EA + L+ LR + EEL+ I+ ES ++ G + Sbjct: 197 FLPNSPRWLAEKGRHIEAEEVLRMLRDTSEKAREELNEIR----ESLKLKQGGWALFKIN 252 Query: 277 KNHIKPVFISLGLMFFQQFSGINAVIFYTVQIFKDSGSTVDEN--LSTIIVGLVNFISTF 334 +N + VF+ + L QQF+G+N +++Y +IFK +G T E ++T++VGL +TF Sbjct: 253 RNVRRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIATLVVGLTFMFATF 312 Query: 335 VAAMIIDRLGRKMLLYISSILMCITLFTFGTFFYVKELMDVTA---FGWIPLMSLIVYVI 391 +A +D+ GRK L I +M + G + + + + TA W+ + ++ + Sbjct: 313 IAVFTVDKAGRKPALKIGFSVMALGTLVLG--YCLMQFDNGTASSGLSWLSVGMTMMCIA 370 Query: 392 GFSFGFGPIPWLMMGEILPVKIRGTAASVATAFNWSCTFVVTKTYEDLVLHIGPYGTFWL 451 G++ P+ W++ EI P+K R + +T NW ++ T+ L+ IG GTFWL Sbjct: 371 GYAMSAAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLDSIGAAGTFWL 430 Query: 452 FGTLVAVAFIFVII-CVPETRGRSLEEIERR 481 + T + +AF+ + +PET+ +LE IER+ Sbjct: 431 Y-TALNIAFVGITFWLIPETKNVTLEHIERK 460 Lambda K H 0.327 0.141 0.425 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: 608 Number of extensions: 31 Number of successful extensions: 6 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: 502 Length of database: 472 Length adjustment: 34 Effective length of query: 468 Effective length of database: 438 Effective search space: 204984 Effective search space used: 204984 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 (21.7 bits) S2: 52 (24.6 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