Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BPHYT_RS16060 BPHYT_RS16060 ribonucleotide-diphosphate reductase subunit alpha
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__BFirm:BPHYT_RS16060 Length = 506 Score = 428 bits (1100), Expect = e-124 Identities = 223/493 (45%), Positives = 329/493 (66%), Gaps = 3/493 (0%) Query: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 ++ L N+ K FPGV AL E+ GE+HAL+GENGAGKSTLMKIL G+YQ D G I + Sbjct: 4 ILKLDNITKSFPGVKALQGIHLEIERGEIHALLGENGAGKSTLMKILCGIYQPDEGTITI 63 Query: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141 +G+ + A A G+GI+ QE +L+ +L+A +N+F+GRE + +GL ++ ++ R A Sbjct: 64 EGEARHFSNYHDAVAAGVGIVFQEFSLIPYLNAVENMFLGRELKNGLGL-LERGKMRRAA 122 Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 AAIF R+ + +D S P+ EL+VA+QQ VEI KALS ++R+LI+DEPTA L AE LF Sbjct: 123 AAIFQRLGVTIDLSVPIRELSVAQQQFVEIGKALSLEARILILDEPTATLTPAEAEHLFA 182 Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 I+R+L+ QGV +++ISH ++E+ ++ DR++V+RDG+Y+ + ++++ ++ MMVGR + Sbjct: 183 IMRELKQQGVAMIFISHHLEEIFEVCDRITVLRDGQYVGMTEVAQSNVGHLVEMMVGRRI 242 Query: 262 DGE-QRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIF 320 + PP + +VL+V L + +SFTLR+GEILGFAGL+G+GRTE A A+ Sbjct: 243 ENSFPPKPPLRADAKIVLDVEKLQLLKDSPVLSFTLREGEILGFAGLVGSGRTETALAVI 302 Query: 321 GADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF 380 GADP EI I+G A + PADA+ G+G L E RK GL ++ NI+++++G++ Sbjct: 303 GADPAYVKEIRINGTAAKLSDPADALRAGVGILPESRKTEGLITDFSIKQNISINNLGKY 362 Query: 381 TRVG-FMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFF 439 + F+DQR+ A ++++ +K P++ + LSGGNQQK+VIA+WL +IL F Sbjct: 363 RSLRFFIDQRSEARATADIMKRVGVKAPTMHTEVATLSGGNQQKVVIARWLNHHTNILIF 422 Query: 440 DEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELAR 499 DEPTRGIDVGAK+EIY L+ L +G +I+MISSELPE++ M RV V +GRI L Sbjct: 423 DEPTRGIDVGAKAEIYLLMRELTARGYSIIMISSELPEIVGMCDRVAVFRQGRIEAMLEG 482 Query: 500 ADATQEKIMQLAT 512 +M AT Sbjct: 483 DAIDSNAVMTYAT 495 Score = 80.5 bits (197), Expect = 1e-19 Identities = 61/246 (24%), Positives = 117/246 (47%), Gaps = 13/246 (5%) Query: 275 DVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEI 330 D +L++ + + +A++ + + +GEI G GAG++ + + + G + G I Sbjct: 2 DTILKLDNITKSFPGVKALQGIHLEIERGEIHALLGENGAGKSTLMKILCGIYQPDEGTI 61 Query: 331 IIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTR--VGFMDQ 388 I G + DAVA G+G + ++ F L ++ N+ L GR + +G +++ Sbjct: 62 TIEGEARHFSNYHDAVAAGVGIVFQE---FSLIPYLNAVENMFL---GRELKNGLGLLER 115 Query: 389 RAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDV 448 +R AA ++L + T + R LS QQ + I K L + IL DEPT + Sbjct: 116 GKMRRAAAAIFQRLGV-TIDLSVPIRELSVAQQQFVEIGKALSLEARILILDEPTATLTP 174 Query: 449 GAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIM 508 ++ ++ L +QG A++ IS L E+ + R+ V+ +G+ G A + ++ Sbjct: 175 AEAEHLFAIMRELKQQGVAMIFISHHLEEIFEVCDRITVLRDGQYVGMTEVAQSNVGHLV 234 Query: 509 QLATQR 514 ++ R Sbjct: 235 EMMVGR 240 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: 608 Number of extensions: 28 Number of successful extensions: 8 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: 520 Length of database: 506 Length adjustment: 35 Effective length of query: 485 Effective length of database: 471 Effective search space: 228435 Effective search space used: 228435 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