Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 382 bits (981), Expect = e-110 Identities = 219/495 (44%), Positives = 298/495 (60%), Gaps = 6/495 (1%) Query: 5 TPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 TP RGI K FPGVKAL D+SF Y G+VH L+GENGAGKS+L+K+L G Y G Sbjct: 8 TPLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEF 67 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKG--GIVNRSLLNY 122 +G ++ + + G+A+I+QE LVP + +A+NI+LG+ P G V+ + ++ Sbjct: 68 YHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHA 127 Query: 123 EAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNL 182 EA L LGM++ TP+ L + Q QMVEIAKAL++NA+I+ DEPT++LS RE + L Sbjct: 128 EARRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKL 187 Query: 183 FRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVG 242 F VI L+ +G ++Y+SHRM E+FAL D IT+ +DGR V D LV MVG Sbjct: 188 FAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATP-DELVARMVG 246 Query: 243 RDIGDIYGWQPRSY-GEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKG 301 R + Y + + GE L + V A I+L VR+GEIVGL GLVG+GRSE+ + Sbjct: 247 RKVDMSYSRERSAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARA 306 Query: 302 MFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARR 361 +FG I G++YI + + P A G L PE RK+EG+ + +VRDN+ ++ R Sbjct: 307 VFGADPIRQGEIYIFGKRLT-GGPDRARELGAALIPESRKSEGLALIRTVRDNLLLAGLR 365 Query: 362 KHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVI 421 + E A+ I L I TP QL LSGGNQQK ++G+WL E K+ Sbjct: 366 R-AFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKLF 424 Query: 422 LLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481 + DEPTRGIDVGAK EI+ +I +L QG VL SS+LPE++ V DR VMR G IAGE+ Sbjct: 425 IFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGEV 484 Query: 482 LHEQADERQALSLAM 496 H + E + L L M Sbjct: 485 AHAEMTEERILQLGM 499 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: 704 Number of extensions: 41 Number of successful extensions: 10 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: 504 Length of database: 502 Length adjustment: 34 Effective length of query: 470 Effective length of database: 468 Effective search space: 219960 Effective search space used: 219960 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