Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate SM_b20507 SM_b20507 L-arabinose transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Smeli:SM_b20507 Length = 508 Score = 485 bits (1249), Expect = e-141 Identities = 248/499 (49%), Positives = 346/499 (69%), Gaps = 2/499 (0%) Query: 7 YLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVI 66 +L F+ I K +PGV+AL+++SF G VH LMGENGAGKSTL+++LSG+ A TG + I Sbjct: 4 FLEFQSISKGYPGVQALSEVSFSVRKGAVHGLMGENGAGKSTLIRVLSGDQAADTGEIRI 63 Query: 67 NGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGL 126 NG+ + A NAGV +I+QEL LVPE+TVAEN++LG+ P K G+++R L Sbjct: 64 NGEPQHYRSVRDAFNAGVIVIHQELQLVPELTVAENLWLGRFPGKAGVIDRRQLIRVVSD 123 Query: 127 QLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186 +L +G+D+DP+ + LSIG+ QMVEIAKA+ +A++IA DEPTSSLS+RE + LF +I Sbjct: 124 RLAEIGIDVDPEAKVASLSIGERQMVEIAKAVMTDARVIALDEPTSSLSSRESEILFALI 183 Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246 LR G VILYVSHR++EIF L +++TV +DGR D+ +V + ++ MVGR+I Sbjct: 184 DRLRSNGTVILYVSHRLDEIFRLCNSLTVLRDGRLAAHHPDISKVGREQIIAEMVGREIS 243 Query: 247 DIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGT 306 +I+GW+ R+ G RL ++ V + PIS VR+GEI+G FGL+GAGRSE+ + ++G Sbjct: 244 NIWGWRARTLGAARLTVERVSGANLPQPISFTVRAGEILGFFGLIGAGRSEMARLVYGAD 303 Query: 307 QITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLG 366 + G+V +D + P +I AG++LCPEDRK +GI+ S+ +N+ IS+RR H Sbjct: 304 RRRQGKVLVDGLAVPADSPRLSIRAGVVLCPEDRKFDGIVQGRSIEENMAISSRR-HFSP 362 Query: 367 GCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEE-MKVILLDE 425 V++ G E A+ I L ++TP Q I+NLSGGNQQK ILGRWLSEE +KV+L+DE Sbjct: 363 FGVVDKGKEAELAERFIAKLRVRTPSRHQDIVNLSGGNQQKVILGRWLSEEGVKVLLIDE 422 Query: 426 PTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQ 485 PTRGIDVGAK EIY ++Y LAAQG+A++ SS+LPEV+G+ADRI+VM EG IA E+ Sbjct: 423 PTRGIDVGAKSEIYEILYELAAQGMAIVVISSELPEVMGIADRILVMCEGRIAAEIDRSD 482 Query: 486 ADERQALSLAMPKVSQAVA 504 DE + L+ A+P S A Sbjct: 483 FDEHRILAAALPDASATTA 501 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: 699 Number of extensions: 28 Number of successful extensions: 7 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: 508 Length adjustment: 34 Effective length of query: 470 Effective length of database: 474 Effective search space: 222780 Effective search space used: 222780 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