Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__azobra:AZOBR_RS06625 Length = 511 Score = 297 bits (761), Expect = 5e-85 Identities = 189/513 (36%), Positives = 285/513 (55%), Gaps = 23/513 (4%) Query: 21 PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80 P + R V K F A + + G +H ++GENGAGKST+M I+ G D G IL Sbjct: 6 PALETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTIL 65 Query: 81 LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREP--RKAMGLFIDEDELN 138 +DG+PV + PR A A GIG++HQ L++ + +N+ +G E A G+ EL Sbjct: 66 VDGRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGAEGGVTLAAGMARARTELT 125 Query: 139 RQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAE 198 R A L++D PVGEL V QQ VEI KAL + +LI+DEPT L E Sbjct: 126 RLARDY----GLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETDH 181 Query: 199 LFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258 LFRI+R L+ QG +V I+HK+ E+ ++ D V+VMR G+ +A V TS + + +MVG Sbjct: 182 LFRILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMVG 241 Query: 259 R-ALDGEQRIPPDTSRNDVVLEVRGL----NRG-RAIRDVSFTLRKGEILGFAGLMGAGR 312 R L +++P + VLEV GL G ++ + T+R GEI+G AG+ G G+ Sbjct: 242 RKVLLRVEKVP--ATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQ 299 Query: 313 TEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAH-----GIGYLSEDRKHFGLAVGMD 367 +E+ A+ G P G + + G+ + +P A G+G++ EDR+ GL G + Sbjct: 300 SELLEALAGMRPPAEGSVRLR-GEELTATPDRFTARGLRALGVGHVPEDRQRVGLVTGFE 358 Query: 368 VQANIALSSMG--RFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIV 425 Q L G F MD+RA+ + + ++ A SGGNQQKIV Sbjct: 359 AQECAILGHQGDPAFNGRLLMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQKIV 418 Query: 426 IAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRV 485 +A+ + R+ D+L +PTRG+D+GA I++ L AL +QGKAI+++S EL E+ +S R+ Sbjct: 419 LAREMERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRI 478 Query: 486 LVMCEGRITGELARADATQEKI-MQLATQRESA 517 LVM +GR+ GE+A +A + ++ + +A E+A Sbjct: 479 LVMFDGRLVGEVAPGEADERRLGLMMAGVAEAA 511 Lambda K H 0.320 0.135 0.372 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: 711 Number of extensions: 39 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 520 Length of database: 511 Length adjustment: 35 Effective length of query: 485 Effective length of database: 476 Effective search space: 230860 Effective search space used: 230860 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 (21.8 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