Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 363 bits (932), Expect = e-105 Identities = 205/481 (42%), Positives = 300/481 (62%), Gaps = 7/481 (1%) Query: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNY-APTTGSV 64 P L +GI KTF G++ L + Y G++HALMGENGAGKSTL+KILSG Y A G + Sbjct: 5 PLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEI 64 Query: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEA 124 I GQ + D A G+A+IYQEL L P ++VAENIYLG+ +G ++R + Sbjct: 65 RIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWTIDRKGMEAGC 124 Query: 125 GLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFR 184 L+ LG + P T + LSI + Q+VEIA+AL +AKI+ DEPT+ LS+RE D LF Sbjct: 125 IEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFA 184 Query: 185 VIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRD 244 +I++LR +G I+Y+SHRM EI+ALSD ++V +DG Y+ T + +ALV+ MVGRD Sbjct: 185 LIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELT-RDALSAEALVKMMVGRD 243 Query: 245 IGDIYGWQPRSY--GEERLRL-DAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKG 301 + Y + +Y G +R+ D VR S + +GE++G+ GLVGAGR+EL + Sbjct: 244 LSGFYKKEHAAYNPGNVVMRVRDMADGKRVR-HCSFDLHAGEVLGIAGLVGAGRTELARL 302 Query: 302 MFGGTQITAGQVYIDQQPI-DIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISAR 360 +F T+G + + + + +R P+ AI AG++ EDRKA+G+ SV DNIN+ A Sbjct: 303 IFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNINVCAC 362 Query: 361 RKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKV 420 G V++ ++ I+SL+I+ + LSGGNQQK +L R L + V Sbjct: 363 VPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEVKPHV 422 Query: 421 ILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGE 480 ++LDEPTRG+D+G+K EIY +I LA G+ ++ SS+LPE++G DR+++MREG++ E Sbjct: 423 LILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQLVAE 482 Query: 481 L 481 + Sbjct: 483 V 483 Score = 77.4 bits (189), Expect = 1e-18 Identities = 63/218 (28%), Positives = 102/218 (46%), Gaps = 22/218 (10%) Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQIT-AGQVYIDQQPIDIRKPSHAIAAG- 332 + L V GEI L G GAG+S LMK + G Q G++ I Q I P+ A A G Sbjct: 25 VGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEIRIAGQLIPTFDPATAKALGI 84 Query: 333 ------MMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSL 386 + LCP AE I +R I RK + GC+ ++ L Sbjct: 85 AVIYQELSLCPNLSVAENIYLGRELRRGWTID--RKGMEAGCI-----------EVLQRL 131 Query: 387 NIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALA 446 + A + + +LS +Q + R L K++++DEPT + ++ +I L Sbjct: 132 GAEFTPATR-VSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFALIKQLR 190 Query: 447 AQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHE 484 +QG+A+++ S + E+ ++DR+ V+R+G GEL + Sbjct: 191 SQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRD 228 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: 752 Number of extensions: 36 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: 510 Length adjustment: 34 Effective length of query: 470 Effective length of database: 476 Effective search space: 223720 Effective search space used: 223720 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