Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 340 bits (871), Expect = 9e-98 Identities = 195/491 (39%), Positives = 293/491 (59%), Gaps = 6/491 (1%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 L+ G+GKT+ L ++S AG+V AL GENGAGKSTL K++SG PTTG + Sbjct: 17 LAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYR 75 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127 GQ + A GV ++ QEL+L+P +TVAEN++L LP + G ++ L A Sbjct: 76 GQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQLATAA 135 Query: 128 LKHLGMD-IDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186 + +G+D IDPDTP+ L IG QMVEIA+ L + ++ DEPT+ L+ARE+ LF I Sbjct: 136 MARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQI 195 Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246 LR G I+Y+SHR+EE+ ++ I V +DG+ V +Q+ LV MVGR++G Sbjct: 196 ERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCD-EPIQRYSSAELVNLMVGRELG 254 Query: 247 DIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGT 306 + R G L++D + +S VR+GEI G+ GL+GAGR+EL++ ++G Sbjct: 255 EHIDLGRRQLGAPLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGAD 314 Query: 307 QITAGQVYIDQQP--IDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364 + +G + + Q P + I P A+ AG+ L EDRK EG++ S+ NI + Sbjct: 315 RADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAVS 374 Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424 G V+++ E+ A+ I+++ I++ GA+Q++ LSGGNQQK ++GRWL + +V+L D Sbjct: 375 RAG-VLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFD 433 Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHE 484 EPTRGIDVGAK +IY ++ LA QG A++ SSDL E++ + DRI V+ G + + Sbjct: 434 EPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFARD 493 Query: 485 QADERQALSLA 495 + Q L+ A Sbjct: 494 HWSQDQLLAAA 504 Score = 85.1 bits (209), Expect = 5e-21 Identities = 60/229 (26%), Positives = 109/229 (47%), Gaps = 14/229 (6%) Query: 25 DISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVING--QEMSFSDTTAALNA 82 ++SF+ AG++ + G GAG++ LL+++ G +G + + Q +S AA+ A Sbjct: 282 EVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRA 341 Query: 83 GVAIIYQELH---LVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQLKHLGMDI---- 135 G+A+I ++ L+ +++ NI LG L G + +L+ EA L + Sbjct: 342 GIALITEDRKGEGLLLTQSISANIALGNL---GAVSRAGVLDSEAEKALAERQIQAMRIR 398 Query: 136 --DPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEG 193 + LS G Q V I + L R+ +++ FDEPT + +++ ++ EL ++G Sbjct: 399 SAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQG 458 Query: 194 RVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVG 242 + ++ VS + E+ + D I V GR + TF L A G Sbjct: 459 KALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLLAAAFAG 507 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: 686 Number of extensions: 28 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: 524 Length adjustment: 35 Effective length of query: 469 Effective length of database: 489 Effective search space: 229341 Effective search space used: 229341 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