Align ABC transporter related (characterized, see rationale)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 370 bits (950), Expect = e-107 Identities = 199/493 (40%), Positives = 310/493 (62%), Gaps = 8/493 (1%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 + E++ I K++PGVKAL+DVS ++ GEVH LLGENGAGKS+L+KV+ G D G+ Sbjct: 10 LFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYH 69 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRL--GLIHFKKMYADA 121 G P +P D GI+ ++QE +LVP L +AQN+FLG EPR G + +M+A+A Sbjct: 70 DGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHAEA 129 Query: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181 R +L +++ P+ +A QQ++ IA+ ++ +A++LVLDEPTA+L +E + LF Sbjct: 130 RRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLFA 189 Query: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSL 241 ++ +LKA GV++++I+H + +V+ + DRIT+LR+G+ +G L + +L+ M+GR + Sbjct: 190 VIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGRKV 249 Query: 242 QEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301 +ER+ E V L + +VS I +NL V G+ VGLAGL+GSGRSEV Sbjct: 250 DMSY----SRERSAQPGE-VALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVA 304 Query: 302 NAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILAL 361 AVFG D + G I++ G++L P A G AL PE RK +G+ ++R+N++LA Sbjct: 305 RAVFGADPIRQGEIYIFGKRLT-GGPDRARELGAALIPESRKSEGLALIRTVRDNLLLAG 363 Query: 362 QARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPIL 421 R R+ + + +A+ I +L+IATPD ++ + LSGGNQQK+++ +WL E L Sbjct: 364 LRRAFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVAEAKL 423 Query: 422 LVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRE 481 + DEPTRGID+GA AEI LI +L +G +L+ SSEL E++ ++ V+R E Sbjct: 424 FIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGRIAGE 483 Query: 482 LSGAELTSQHVMQ 494 ++ AE+T + ++Q Sbjct: 484 VAHAEMTEERILQ 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: 609 Number of extensions: 31 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