Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6034 Length = 517 Score = 336 bits (862), Expect = 1e-96 Identities = 193/473 (40%), Positives = 278/473 (58%), Gaps = 6/473 (1%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 LS GIGKT+ LT I G+V AL GENGAGKSTL KI+ G APTTG + Sbjct: 10 LSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRFQ 68 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127 G++ + A G+ ++ QEL+L+P ++VAEN++L LP GG ++R L A Sbjct: 69 GRDYRPGSRSQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQLRKAAIEA 128 Query: 128 LKHLGMD-IDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186 + +G+D IDPDT + L IG QMVEIA+ L + ++ DEPT+ L+ARE++ LF I Sbjct: 129 MAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQI 188 Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246 L+ G I+Y+SHR+EE+ ++ I V +DG V M + + LV MVGR++G Sbjct: 189 TRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLV-CVEPMANYNSEQLVTLMVGRELG 247 Query: 247 DIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGT 306 + PR G L + + +S VR+GEI G+ GL+GAGR+EL++ +FG Sbjct: 248 EHIDMGPRKIGAPALTVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGAD 307 Query: 307 QITAGQVYI--DQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364 +G V + Q + IR P+ A+ G+ L EDRK EG++ S+ NI + + Sbjct: 308 TADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALG-NMPVI 366 Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424 G +NNG E + A I ++ I++ QL+ LSGGNQQK ++GRWL + V+L D Sbjct: 367 SSGGFVNNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCTVMLFD 426 Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEI 477 EPTRGIDVGAK +IY ++ L QG A++ SSDL E++ + DRI V+ G + Sbjct: 427 EPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRL 479 Score = 94.0 bits (232), Expect = 1e-23 Identities = 71/246 (28%), Positives = 118/246 (47%), Gaps = 14/246 (5%) Query: 11 RGIGKTFPGVKALT------DISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 R IG VK LT D+SF+ AG++ + G GAG++ LL+++ G +G+V Sbjct: 255 RKIGAPALTVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADTADSGTV 314 Query: 65 VI--NGQEMSFSDTTAALNAGVAIIYQELH---LVPEMTVAENIYLGQLP--HKGGIVNR 117 + + Q +S A+ G+A+I ++ L+ +++ NI LG +P GG VN Sbjct: 315 ALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMPVISSGGFVNN 374 Query: 118 SLLNYEAGLQLKHLGMDIDPDTPL-KYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSA 176 A Q+ + + T L LS G Q V I + L R+ ++ FDEPT + Sbjct: 375 GDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCTVMLFDEPTRGIDV 434 Query: 177 REIDNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDAL 236 +++ ++ EL ++G+ ++ VS + E+ + D I V GR + TF D L Sbjct: 435 GAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLL 494 Query: 237 VQAMVG 242 A G Sbjct: 495 AAAFAG 500 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: 654 Number of extensions: 27 Number of successful extensions: 10 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: 517 Length adjustment: 35 Effective length of query: 469 Effective length of database: 482 Effective search space: 226058 Effective search space used: 226058 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