Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate GFF2770 PGA1_c28130 ABC transporter, ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Phaeo:GFF2770 Length = 505 Score = 253 bits (645), Expect = 1e-71 Identities = 159/480 (33%), Positives = 259/480 (53%), Gaps = 13/480 (2%) Query: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65 P LS +G+ K +PGV A +SFD AG+VHAL+GENGAGKSTL+K++ G P +G ++ Sbjct: 4 PLLSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKML 63 Query: 66 INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAG 125 ++G+ + + A G+A+++Q L + VAENI LG + R L Sbjct: 64 LHGEPYTPGEPRQARADGIAMVFQHFSLFDALNVAENIALGM---ETPPALRDLATQIRK 120 Query: 126 LQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRV 185 + + G+ +DP + LS G+ Q VEI + L ++ K++ DEPTS L+ +E++ LF+ Sbjct: 121 VS-ETYGLPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFQT 179 Query: 186 IRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDI 245 +++LR EG ILY+SH++EEI L D T+ + G+ V + D + + MVG + Sbjct: 180 LQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARD-MAEMMVGTAL 238 Query: 246 GDIYGWQPRSYGEERLRLDAVKAPG------VRTPISLAVRSGEIVGLFGLVGAGRSELM 299 R+ G+ L + + P + + VR GEI+G+ G+ G G+ EL+ Sbjct: 239 -QTPERSGRALGDVALDISGLSVPAPSAFGTALKNVHMTVRKGEILGVGGVAGNGQDELL 297 Query: 300 KGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINI-S 358 + G T A V +D PI P G++ PE+R P S+ +N + + Sbjct: 298 GVLSGETTTAADAVTLDGAPIGNLGPVARRRLGILAAPEERLGHAAAPDMSLTENAMLTA 357 Query: 359 ARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEM 418 A R+ + + G + A+ I+S +++TPG E +LSGGN QK ++GR + + Sbjct: 358 ATREGLASRGFLKWGLAQEFAEKVIKSFDVRTPGPENAARSLSGGNLQKFVIGREVLQRP 417 Query: 419 KVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIA 478 V+++++PT G+D A I + LAA G AV+ S DL E++ +AD + EG ++ Sbjct: 418 DVLVVNQPTWGVDAAAAAAIRQSLLDLAAGGTAVICISQDLDELMEIADSFAALNEGRLS 477 Score = 63.9 bits (154), Expect = 1e-14 Identities = 52/227 (22%), Positives = 106/227 (46%), Gaps = 21/227 (9%) Query: 269 PGV--RTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPS 326 PGV +S + +GE+ L G GAG+S L+K ++G + +G++ + +P +P Sbjct: 16 PGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKMLLHGEPYTPGEPR 75 Query: 327 HAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSL 386 A A G+ + + + +V +NI + L + IR + Sbjct: 76 QARADGIAMVFQHFS---LFDALNVAENIALGMETPPAL-----------RDLATQIRKV 121 Query: 387 NIKTPGAE----QLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVI 442 + +T G + + +LS G +Q+ + R L ++ K++++DEPT + ++ + Sbjct: 122 S-ETYGLPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFQTL 180 Query: 443 YALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADER 489 L ++G ++L+ S L E+ + D ++R G+ GE + + R Sbjct: 181 QKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSAR 227 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: 610 Number of extensions: 33 Number of successful extensions: 7 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: 505 Length adjustment: 34 Effective length of query: 470 Effective length of database: 471 Effective search space: 221370 Effective search space used: 221370 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