Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 345 bits (886), Expect = 2e-99 Identities = 204/516 (39%), Positives = 307/516 (59%), Gaps = 30/516 (5%) Query: 4 STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63 S P L+ RG+ K F GV+AL + F G++HAL+GENGAGKSTL+K L+G Y G+ Sbjct: 9 SPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGT 68 Query: 64 VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYE 123 V + G+ ++ A + +YQE++L+P ++VAEN++LG+ P + G+V+R + Sbjct: 69 VTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRR 128 Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183 A L G+ +D PL S+ Q+V IA+A+ +AK++ DEPT+SL A+E+ LF Sbjct: 129 ARAVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLF 188 Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYV--KTFTDMQQVDHDALVQAMV 241 +V+R LR G I++V+H +++++AL D ITV ++GR V + ++ ++D LV M+ Sbjct: 189 KVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLD---LVAMML 245 Query: 242 GRDIGDIYG--WQPRSYGEERLRLDAVKAPGVR-----TPISLAVRSGEIVGLFGLVGAG 294 GR++ + P EE R V+ G P L +R GE+VGL GL+G+G Sbjct: 246 GRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSG 305 Query: 295 RSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDN 354 R+E + +FG + G+ +D Q + +R P AI G CPEDRK EGI+ SVR+N Sbjct: 306 RTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVREN 365 Query: 355 INISARRKHVLGGCVINNGW--------EENNADHHIRSLNIKTPGAEQLIMNLSGGNQQ 406 I ++ + + GW +E AD IR L+I+TP AEQ I LSGGNQQ Sbjct: 366 IILALQAR---------QGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQ 416 Query: 407 KAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVA 466 KA+L RWL+ E ++++LDEPTRGIDVGA EI +I L A G+A+L SS+L E++ + Sbjct: 417 KALLARWLATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYS 476 Query: 467 DRIVVMREGEIAGELL-HEQADERQALSLAMPKVSQ 501 R+VV+R+ EL E A +R ++A V + Sbjct: 477 RRVVVLRDRRHVAELRGGEVAVDRIVAAIASESVPE 512 Score = 70.9 bits (172), Expect = 1e-16 Identities = 60/233 (25%), Positives = 106/233 (45%), Gaps = 13/233 (5%) Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMM 334 + VR GEI L G GAG+S L+K + G Q AG V ++ + I R A + Sbjct: 31 VDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTLEGRAIAPRGVEEAQRLHIG 90 Query: 335 LCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIR---SLNIKTP 391 ++ ++P SV +N+ + R+ + G V I +L++ P Sbjct: 91 TVYQE---VNLLPNLSVAENLFLG--RQPMRFGLVDRGAMRRRARAVLIPYGLTLDVTAP 145 Query: 392 GAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVA 451 + S QQ + R + KV++LDEPT +D ++ V+ L ++G+ Sbjct: 146 -----LGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFKVMRTLRSRGIG 200 Query: 452 VLFASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSLAMPKVSQAVA 504 ++F + L +V + DRI V+R G + GE + +++ + + +AVA Sbjct: 201 IVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGRELEAVA 253 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: 635 Number of extensions: 31 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