Align deoxynucleoside transporter, ATPase component (characterized)
to candidate BPHYT_RS16060 BPHYT_RS16060 ribonucleotide-diphosphate reductase subunit alpha
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__BFirm:BPHYT_RS16060 Length = 506 Score = 320 bits (820), Expect = 8e-92 Identities = 188/489 (38%), Positives = 278/489 (56%), Gaps = 11/489 (2%) Query: 16 LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75 L++ + K F GV AL+G+ L +RG+I+ LLGENG GKSTL+KI+ G PDEG + IE Sbjct: 5 LKLDNITKSFPGVKALQGIHLEIERGEIHALLGENGAGKSTLMKILCGIYQPDEGTITIE 64 Query: 76 GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135 G + +A+AAG+ V+Q+ SL+P ++ EN+ L EL G L R RR AA Sbjct: 65 GEARHFSNYHDAVAAGVGIVFQEFSLIPYLNAVENMFLGRELKNGLGLLERGKMRRAAAA 124 Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195 R + L S I +L +A +Q V I +A++ EA+ +I+DEPT +LT E Sbjct: 125 IFQRLGVTIDL-------SVPIRELSVAQQQFVEIGKALSLEARILILDEPTATLTPAEA 177 Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255 ++L A++ L+ QGV ++F+SH L+E + + + VLRDGQ + +A+ + E+M Sbjct: 178 EHLFAIMRELKQQGVAMIFISHHLEEIFEVCDRITVLRDGQYVGMTEVAQSNVGHLVEMM 237 Query: 256 TGRHLSNERYRESAHAQD--IVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNEL 313 GR + N + D IVLDV +SF L GEILG GL+ SGR E Sbjct: 238 VGRRIENSFPPKPPLRADAKIVLDVEKLQLLKDSPVLSFTLREGEILGFAGLVGSGRTET 297 Query: 314 ARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITA 373 A A+ G PA ++ ++G L P+DA R +G +PE R EGL D I+ N+ Sbjct: 298 ALAVIGADPAYVKEIRINGTAAKLSDPADALRAGVGILPESRKTEGLITDFSIKQNISIN 357 Query: 374 MISSLRD-RFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAID 432 + R RF R+ A+A A+ +K + + P + V +LSGGNQQ+V+I RWL Sbjct: 358 NLGKYRSLRFFIDQRSEARATAD-IMKRVGVKAPTMHTEVATLSGGNQQKVVIARWLNHH 416 Query: 433 PRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHV 492 +LI PT G+DVG+K IY +M+ L+ RG II+IS +LPE++ CDR+ + ++G + Sbjct: 417 TNILIFDEPTRGIDVGAKAEIYLLMRELTARGYSIIMISSELPEIVGMCDRVAVFRQGRI 476 Query: 493 SAEYRADEL 501 A D + Sbjct: 477 EAMLEGDAI 485 Lambda K H 0.319 0.135 0.376 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: 554 Number of extensions: 24 Number of successful extensions: 6 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: 515 Length of database: 506 Length adjustment: 35 Effective length of query: 480 Effective length of database: 471 Effective search space: 226080 Effective search space used: 226080 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