Align ABC transporter related (characterized, see rationale)
to candidate GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__WCS417:GFF3463 Length = 502 Score = 357 bits (915), Expect = e-103 Identities = 198/501 (39%), Positives = 307/501 (61%), Gaps = 7/501 (1%) Query: 1 MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60 MS +L+L+ I K YPGV+AL+ ++L++ GE+HALLGENGAGKSTL+K++ G + +D G Sbjct: 1 MSSLLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQ 60 Query: 61 ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYE-PRRLGLIHFKKMYA 119 IL G+ Q F T DA AGI V+QE +L+P LT +N+FLG+E R GL+ ++M Sbjct: 61 ILIDGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVE 120 Query: 120 DARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179 + A+ + + ID+ + S+A QQ + IA+ +A+ A++LVLDEPTA+L E ++L Sbjct: 121 ASEALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELL 180 Query: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239 F I+ +LK +GVA++FI+H L++++Q+ DRI+VLR+G +G A+ L+E M+GR Sbjct: 181 FEIMRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGR 240 Query: 240 SLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSE 299 L K +ER +LL ++D+ + + + KG+ +G AGL+GSGR+E Sbjct: 241 RLACSFPPKPTRER-----GPLLLEVKDIQLVRNGPHNRFQLHKGEILGFAGLVGSGRTE 295 Query: 300 VCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIIL 359 + + G S + L G+K+ L P A++ GI L PE RK +G+I SIRENI L Sbjct: 296 LALGMMGALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISL 355 Query: 360 -ALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIE 418 L + R+ + + +L I P ++ + LSGGNQQKV++ARW+ Sbjct: 356 NNLPKYQNASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHH 415 Query: 419 PILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYA 478 +LV DEPTRGID+GA A+I L+R+L ++G ++++ SSEL E++ ++V V Sbjct: 416 CDVLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAI 475 Query: 479 VRELSGAELTSQHVMQAIAEG 499 V+ L + + Q VM+ G Sbjct: 476 VKLLEASAVNPQEVMRHATGG 496 Lambda K H 0.319 0.136 0.377 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: 534 Number of extensions: 24 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: 499 Length of database: 502 Length adjustment: 34 Effective length of query: 465 Effective length of database: 468 Effective search space: 217620 Effective search space used: 217620 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