Align ABC transporter related (characterized, see rationale)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 Length = 514 Score = 328 bits (840), Expect = 4e-94 Identities = 185/492 (37%), Positives = 306/492 (62%), Gaps = 8/492 (1%) Query: 5 LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL 64 L I K +PGVKAL+++S G+VHAL+GENGAGKSTL+K++ GA + G + Sbjct: 16 LRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIG 75 Query: 65 GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAV 124 F + D+ +G++ ++QE++LVP +TVA+NLFLG+ P GLI+ + A A Sbjct: 76 ERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALAC 135 Query: 125 LTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILN 184 L +ID + S+ +QL+ IA+ ++ A V+ DEPT+SL A+E+ L I+ Sbjct: 136 LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIG 195 Query: 185 QLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEY-LTAELPQPKLIEAMLGRSLQE 243 +L+ +G +++++H +++V++I + +TV ++G+++ + ++L +L+ M+GR +Q+ Sbjct: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVGRDIQD 255 Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303 + D + ++R AV L ++ + G + ++ V KG+ +GL GL+G+GR+E+ Sbjct: 256 -IYDYRPRQR-----GAVALKVDGLLGPGLREPVSFEVHKGEILGLFGLVGAGRTELLRL 309 Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENI-ILALQ 362 + GL +G + L G +L L P DAI+AGI LCPEDRK +GI+ S+ ENI I A Sbjct: 310 LSGLARHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARG 369 Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422 A + L +++ A+ I L++ TP+A + I LSGGNQQK IL RWL++ +L Sbjct: 370 AHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVL 429 Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482 +LDEPTRGIDIGA AEI ++I L EG++++V SS+L E++ S++++VL + EL Sbjct: 430 LLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGEL 489 Query: 483 SGAELTSQHVMQ 494 S + +++Q Sbjct: 490 SREQANESNLLQ 501 Score = 82.0 bits (201), Expect = 5e-20 Identities = 66/232 (28%), Positives = 112/232 (48%), Gaps = 9/232 (3%) Query: 15 PGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPM 74 PG++ E VS + GE+ L G GAG++ L+++++G G + G +P Sbjct: 277 PGLR--EPVSFEVHKGEILGLFGLVGAGRTELLRLLSGLARHSAGQLKLRGHELKLRSPR 334 Query: 75 DAQKAGISTVYQE---VNLVPNLTVAQNLFL---GYEPRRLGLIHFKKMYADARAVLTQF 128 DA AGI ++ ++P +VA+N+ + G L+ +A + Sbjct: 335 DAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNAEQQIKAL 394 Query: 129 KLDIDVSAPLSDY-SIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLK 187 K+ +A Y S QQ + R ++M KVL+LDEPT +D ++ I++ L Sbjct: 395 KVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLA 454 Query: 188 AKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239 A+G+A++ ++ L +V ISDRI VL G GE + + L++ L R Sbjct: 455 AEGIAVIVVSSDLMEVMGISDRILVLCEGALRGELSREQANESNLLQLALPR 506 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: 583 Number of extensions: 33 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 499 Length of database: 514 Length adjustment: 34 Effective length of query: 465 Effective length of database: 480 Effective search space: 223200 Effective search space used: 223200 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