Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 98.2 bits (243), Expect = 3e-25 Identities = 54/199 (27%), Positives = 107/199 (53%), Gaps = 9/199 (4%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 + +++ ++ ++GG++A+ GIDL + GE + L G NGAGK+T +K ++G P +G I Sbjct: 7 LFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEI 66 Query: 65 EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWF 124 + GQPL+ + + + + ++ + + ++S+ EN+ +G + G++ D D + Sbjct: 67 LWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRM--DYDAMY 124 Query: 125 AVFPRLKE-------RAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVE 177 A L + A A GG QQ+ +A+AL KLL+LDEP+ L+ E Sbjct: 125 AKADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETE 184 Query: 178 KIFEVIRNVSAQGITILLV 196 + ++ ++ +G+ + + Sbjct: 185 VLLGIVEDLKRRGVACIYI 203 Score = 87.4 bits (215), Expect = 5e-22 Identities = 65/209 (31%), Positives = 105/209 (50%), Gaps = 18/209 (8%) Query: 21 VKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPA-SRVEGHIEYLGQPLKGKKSFEL 79 V + ++ GE++ + G GAG+T + AI G S VE +E G+PLK + + Sbjct: 282 VDDVSFQLRRGEILGIAGLVGAGRTELVSAIFGAYTGKSSVELFLE--GRPLKIRSPADA 339 Query: 80 VKDKLAMVPEGR---GVFTRMSIQENLLMGAYTSDDKGQIAADIDKW---FAVFPRLKER 133 ++ L MVPE R G+ + + +N+ + D A ID+ A+ ++ ER Sbjct: 340 IRAGLGMVPEDRKRHGIVPLLGVGDNITLATL---DHYAHAGHIDRQRELVAIEAQIAER 396 Query: 134 AAQMAGT------LSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRNVS 187 + A LSGG QQ +A+ L++ PK+L+LDEP+ G+ +I+ +I ++ Sbjct: 397 RVKTASPALPIARLSGGNQQKAVLAKMLLARPKVLILDEPTRGVDVGAKAEIYRLIFELA 456 Query: 188 AQGITILLVEQNAKLALEAAHRGYVMESG 216 AQG+ I+LV L A R VM G Sbjct: 457 AQGVAIVLVSSEMPEVLGMADRVLVMGEG 485 Lambda K H 0.317 0.134 0.365 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: 287 Number of extensions: 14 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: 241 Length of database: 513 Length adjustment: 29 Effective length of query: 212 Effective length of database: 484 Effective search space: 102608 Effective search space used: 102608 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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