Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha
Query= ecocyc::YTFR-MONOMER (500 letters) >FitnessBrowser__WCS417:GFF3463 Length = 502 Score = 353 bits (907), Expect = e-102 Identities = 201/473 (42%), Positives = 294/473 (62%), Gaps = 14/473 (2%) Query: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 +L+ E + K +PGV+AL +++ + RGEI ALLGENGAGKSTL+K L GV H D G I + Sbjct: 4 LLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILI 63 Query: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGRE-PKRFGLLRRKEMEKRAT 127 +GQA A GIG V+QE +L+P ++ +N+F+G E RFGLLR++EM + + Sbjct: 64 DGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVEASE 123 Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187 L G ++D++ + SVA QQ V I +A+ L A++L+LDEPTA+L E ELLF++ Sbjct: 124 ALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELLFEI 183 Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL- 246 MR+L+ +GV++IF++H L++++QV DRI+VLR+G VG + + LV+MM+GR L Sbjct: 184 MRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGRRLA 243 Query: 247 ---DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFD-LEVRPGEIVGLAGLLGSGRTET 302 + G LL K + +N P + ++ GEI+G AGL+GSGRTE Sbjct: 244 CSFPPKPTRERGPLLLEVKDIQLVRN-------GPHNRFQLHKGEILGFAGLVGSGRTEL 296 Query: 303 AEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIIL- 361 A + G P+ S ++G+ L P QA GIG PE RK++G+I S+RENI L Sbjct: 297 ALGMMGALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLN 356 Query: 362 ALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRP 421 L + I + + E ++QL I+ PS+E + LSGGNQQKV+++RW+ Sbjct: 357 NLPKYQNASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHC 416 Query: 422 QFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVII 474 L+ DEPTRGIDVGA A+I L+ +L G A+++ISSEL E++G DRV + Sbjct: 417 DVLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAV 469 Score = 84.7 bits (208), Expect = 7e-21 Identities = 63/226 (27%), Positives = 109/226 (48%), Gaps = 9/226 (3%) Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327 K Y + +L+V GEI L G G+G++ +++ G++ D G LI G+ Q Sbjct: 12 KRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILIDGQAQQFA 71 Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILA--LQAQRGWLRPISRKEQQEIAERF 385 + A GIG ++ +I + ENI L L + G LR ++E E +E Sbjct: 72 TYRDAIAAGIGIVFQEFS---LIPYLTAVENIFLGHELSNRFGLLR---KREMVEASEAL 125 Query: 386 IRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLI 445 ++LG+ T + ++ LS QQ V +++ L + L+LDEPT + + ++ Sbjct: 126 FKRLGV-TIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELLFEIM 184 Query: 446 ETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSV 491 L G+A++ IS LEE+ DR+ ++RD V +A+ + Sbjct: 185 RELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDI 230 Score = 80.9 bits (198), Expect = 1e-19 Identities = 58/221 (26%), Positives = 100/221 (45%), Gaps = 7/221 (3%) Query: 30 FSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGIGTV 89 F L +GEI+ G G+G++ L + G + +WL G+ I+ + A A GIG + Sbjct: 275 FQLHKGEILGFAGLVGSGRTELALGMMGALPSVSKDVWLRGEKITLDDPAQALAHGIGLL 334 Query: 90 YQE---VNLLPNMSVADNLFIGREPK---RFGLLRRKEMEKRATELMASYGFSLDVREP- 142 + L+ + S+ +N+ + PK GL+ + LM E Sbjct: 335 PESRKSEGLITDFSIRENISLNNLPKYQNASGLIDKNRECASVEGLMKQLSIKAPSSESR 394 Query: 143 LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLIFVT 202 + S QQ V I R I+ VL+ DEPT +D ++ LMR L ++G ++I ++ Sbjct: 395 VFNLSGGNQQKVVIARWINHHCDVLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMIS 454 Query: 203 HFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243 L ++ + DR+ V G+ V E + E+++ G Sbjct: 455 SELPEIIGMCDRVAVFHKGAIVKLLEASAVNPQEVMRHATG 495 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: 575 Number of extensions: 25 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 500 Length of database: 502 Length adjustment: 34 Effective length of query: 466 Effective length of database: 468 Effective search space: 218088 Effective search space used: 218088 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