Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Koxy:BWI76_RS14860 Length = 510 Score = 389 bits (999), Expect = e-112 Identities = 217/493 (44%), Positives = 315/493 (63%), Gaps = 10/493 (2%) Query: 4 STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63 S P L GI K + AL ++ FD +AG+VHALMGENGAGKSTL+KILSGN +G Sbjct: 6 SPPLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGV 65 Query: 64 VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHK-GGIVNRSLLNY 122 + I+GQ + A G+AII+QEL+ VP+MTVAEN++LGQ P GI++R ++ Sbjct: 66 IFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMHR 125 Query: 123 EAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNL 182 EA +L + DIDP PL LSIG+ QMVEIA+A++ NAK++ DEPT++LS E L Sbjct: 126 EAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQL 185 Query: 183 FRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVG 242 +R+I ++R++G ++Y+SHRMEE++ L++ +TVF+DG ++ T ++ V +V+ MVG Sbjct: 186 YRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGT-ENLGNVSTTDIVRMMVG 244 Query: 243 RDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGM 302 R I D+Y +PR+ G+ L + + A P+S V +GE+V + GLVG+GR+E+ + + Sbjct: 245 RQIVDLYQHEPRTPGDVLLEVRDL-AGSATGPVSFEVSAGEVVSMSGLVGSGRTEVARLL 303 Query: 303 FGGTQITAGQVYI---DQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISA 359 FG + G V + + QP D P+ AIA G+ + EDRK +G+ HSV NI+IS+ Sbjct: 304 FGADPRSQGSVRLAGRESQPSD---PTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISS 360 Query: 360 RRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMK 419 V GG V+ +R L ++ E + LSGGNQQKA L RWL + + Sbjct: 361 LDNFVAGG-VVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSR 419 Query: 420 VILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAG 479 +++LDEPTRG+D+GAK EIY +I LA G A+L SSDLPE +G++DR++VMR G I Sbjct: 420 LLILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVH 479 Query: 480 ELLHEQADERQAL 492 +L A E + + Sbjct: 480 QLPSCSATEEEVM 492 Score = 88.6 bits (218), Expect = 5e-22 Identities = 58/220 (26%), Positives = 111/220 (50%), Gaps = 6/220 (2%) Query: 26 ISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMSFSDTTAALNAGVA 85 +SF+ AG+V ++ G G+G++ + ++L G + GSV + G+E SD TAA+ G+ Sbjct: 276 VSFEVSAGEVVSMSGLVGSGRTEVARLLFGADPRSQGSVRLAGRESQPSDPTAAIADGIG 335 Query: 86 IIYQELH---LVPEMTVAENIYLGQLPH--KGGIVNRSLLNYEAGLQLKHLGMDIDP-DT 139 ++ ++ L +V NI + L + GG+V R + Q++ L + + + Sbjct: 336 MVTEDRKTQGLFLGHSVEHNIDISSLDNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVEL 395 Query: 140 PLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEGRVILYV 199 P+ LS G Q +A+ L R+++++ DEPT + ++ +I L + G+ IL + Sbjct: 396 PVSALSGGNQQKAALARWLLRDSRLLILDEPTRGVDIGAKREIYELIDRLARAGKAILVI 455 Query: 200 SHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQA 239 S + E +SD + V + GR V + + ++ A Sbjct: 456 SSDLPEAIGISDRVLVMRGGRIVHQLPSCSATEEEVMLHA 495 Lambda K H 0.319 0.136 0.391 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: 689 Number of extensions: 35 Number of successful extensions: 9 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: 504 Length of database: 510 Length adjustment: 34 Effective length of query: 470 Effective length of database: 476 Effective search space: 223720 Effective search space used: 223720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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