Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__BFirm:BPHYT_RS27185 Length = 516 Score = 384 bits (986), Expect = e-111 Identities = 212/490 (43%), Positives = 300/490 (61%), Gaps = 3/490 (0%) Query: 4 STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63 S L +G+ K FPGV AL I D AG+VHA+ GENGAGKSTL+KI+SG Y G Sbjct: 20 SREILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGV 79 Query: 64 VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYE 123 V G + FS T+ A AG+AII+QEL+LVP ++VAENIYL + P +G V+ LN Sbjct: 80 VRYRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNSN 139 Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183 A L+ +G+++ P T + LS+ Q QMVEIAKAL+ +A+++ DEPTSSL+ E LF Sbjct: 140 AQRCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLF 199 Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243 R+IRELR G ILY+SHR++E+ + D +TV +DGR++ T +D + +V MVGR Sbjct: 200 RIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIAT-SDFASTTVNEIVARMVGR 258 Query: 244 DIGDIY-GWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGM 302 + D Y Q + LR+ ++ GV P+S +R GEI+G GL+GAGR+E + + Sbjct: 259 PLDDAYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETARAI 318 Query: 303 FGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRK 362 FG + +G + + +P+ I P AI G+ EDRK +G+ V NI + A + Sbjct: 319 FGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITL-ANVR 377 Query: 363 HVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVIL 422 + + E A+ ++R L I+TP +Q+ NLSGGNQQK ++ +WL +++ Sbjct: 378 AISSRGFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILF 437 Query: 423 LDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELL 482 DEPTRGIDVGAK+ IY ++ LAA GV V+ SS+LPE+LG+ DRI V EG I L Sbjct: 438 FDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLE 497 Query: 483 HEQADERQAL 492 Q + + L Sbjct: 498 TRQTSQEEIL 507 Score = 71.6 bits (174), Expect = 6e-17 Identities = 53/227 (23%), Positives = 106/227 (46%), Gaps = 13/227 (5%) Query: 26 ISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMSFSDTTAALNAGVA 85 +SF+ G++ G GAG++ + + G P +GS+ + + ++ A+ G+A Sbjct: 291 LSFELRKGEILGFAGLMGAGRTETARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIA 350 Query: 86 IIYQELH---LVPEMTVAENIYLGQLPHKGGIVNRSLLNYE-----AGLQLKHLGMDIDP 137 + ++ L M V+ NI L + I +R L + A ++ LG+ Sbjct: 351 YLSEDRKKDGLALSMPVSANITLANVR---AISSRGFLRFSEETAIAERYVRELGIRTPT 407 Query: 138 DTPL-KYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEGRVI 196 + + LS G Q + I+K L R ++I+ FDEPT + ++ ++ L +G + Sbjct: 408 VKQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGV 467 Query: 197 LYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243 + +S + E+ ++D I VF +GR + + +Q + ++ GR Sbjct: 468 VLISSELPELLGMTDRIAVFHEGR-ITAVLETRQTSQEEILHHASGR 513 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: 650 Number of extensions: 19 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: 516 Length adjustment: 34 Effective length of query: 470 Effective length of database: 482 Effective search space: 226540 Effective search space used: 226540 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