Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate BPHYT_RS16060 BPHYT_RS16060 ribonucleotide-diphosphate reductase subunit alpha
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__BFirm:BPHYT_RS16060 Length = 506 Score = 365 bits (938), Expect = e-105 Identities = 209/507 (41%), Positives = 296/507 (58%), Gaps = 29/507 (5%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 IL+ + ++K FPGVKAL + + RGEI ALLGENGAGKSTL+K L G+Y D GTI + Sbjct: 4 ILKLDNITKSFPGVKALQGIHLEIERGEIHALLGENGAGKSTLMKILCGIYQPDEGTITI 63 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKR-FGLLRRKEMEKRAT 127 EG+A N A G+G V+QE +L+P ++ +N+F+GRE K GLL R +M + A Sbjct: 64 EGEARHFSNYHDAVAAGVGIVFQEFSLIPYLNAVENMFLGRELKNGLGLLERGKMRRAAA 123 Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187 + G ++D+ P+ SVA QQ V I +A+ L A++LILDEPTA+L E E LF + Sbjct: 124 AIFQRLGVTIDLSVPIRELSVAQQQFVEIGKALSLEARILILDEPTATLTPAEAEHLFAI 183 Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247 MR+L+ +GV++IF++H L+++++V DRITVLR+G +VG E + LV+MM+GR ++ Sbjct: 184 MRELKQQGVAMIFISHHLEEIFEVCDRITVLRDGQYVGMTEVAQSNVGHLVEMMVGRRIE 243 Query: 248 TH-------------ALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGL 294 L LL D PV +F +R GEI+G AGL Sbjct: 244 NSFPPKPPLRADAKIVLDVEKLQLLKDSPVLSF--------------TLREGEILGFAGL 289 Query: 295 LGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAAS 354 +GSGRTETA + G PA I G L P A G+G PE RKT+G+I S Sbjct: 290 VGSGRTETALAVIGADPAYVKEIRINGTAAKLSDPADALRAGVGILPESRKTEGLITDFS 349 Query: 355 VRENI-ILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLL 413 +++NI I L R I ++ + ++++G++ P+ + LSGGNQQKV++ Sbjct: 350 IKQNISINNLGKYRSLRFFIDQRSEARATADIMKRVGVKAPTMHTEVATLSGGNQQKVVI 409 Query: 414 SRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVI 473 +RWL LI DEPTRGIDVGA AEI L+ L A G ++++ISSEL E+VG DRV Sbjct: 410 ARWLNHHTNILIFDEPTRGIDVGAKAEIYLLMRELTARGYSIIMISSELPEIVGMCDRVA 469 Query: 474 IMRDRKQVAEIPLAELSVPAIMNAIAA 500 + R + A + + A+M A Sbjct: 470 VFRQGRIEAMLEGDAIDSNAVMTYATA 496 Lambda K H 0.321 0.138 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: 592 Number of extensions: 39 Number of successful extensions: 8 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: 500 Length of database: 506 Length adjustment: 34 Effective length of query: 466 Effective length of database: 472 Effective search space: 219952 Effective search space used: 219952 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