Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate GFF100 Psest_0100 phosphonate ABC transporter, ATP-binding protein
Query= uniprot:A0A165ZSX8 (514 letters) >FitnessBrowser__psRCH2:GFF100 Length = 276 Score = 107 bits (266), Expect = 7e-28 Identities = 82/268 (30%), Positives = 137/268 (51%), Gaps = 19/268 (7%) Query: 12 IGGSLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGG-AYIPSSG 70 + ++R + K+F G QAL ++ PG++ AL+G +G+GKSTLL+ L G A SS Sbjct: 1 MNAAIRVERLNKTFAGKQALFDLGLAVQPGEMVALIGASGSGKSTLLRHLAGLACCDSSA 60 Query: 71 DLQI---GEQTMA---FKGTADSIASGVAVIHQELHLVPEMTVAENL---FLGHLPARFG 121 +I G + A G + + + I Q+ +LV ++V +N+ FLG +P G Sbjct: 61 GGRIEVLGREVQATGRLHGEVRRLRADIGYIFQQFNLVTRLSVLDNVLLGFLGRMPRWRG 120 Query: 122 LVN--RGVLRQQALTLLK--GLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDE 177 + ++QA+ L+ GLA+ ++ LS GQ+Q V IA+AL++ A VI DE Sbjct: 121 SLGMFSDEQKRQAMAALERVGLAER--AAQRASTLSGGQQQRVAIARALTQQAEVILADE 178 Query: 178 PTSSLSAREIDRLMAIIGRL-RDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENM 236 P +SL ++M I+ + R +GK V+ H+++ R C+ K GR ++ Sbjct: 179 PIASLDPESARKVMEILADINRQDGKTVVVTLHQVDYALRYCSRAVALKGGRI--HYDGP 236 Query: 237 SELTHDQLVTCMVGRDIQDIYDYRPRER 264 S D+L+ + G D+ + R R Sbjct: 237 SAALSDRLLNDLYGADLDASLLFSDRAR 264 Score = 49.7 bits (117), Expect = 1e-10 Identities = 56/214 (26%), Positives = 95/214 (44%), Gaps = 28/214 (13%) Query: 287 VHKGEILGLFGLVGAGRTELLRLLSGL---ERQREGSLVLHDKELKLRSPRDAIAAGVLL 343 V GE++ L G G+G++ LLR L+GL + G + + +E++ A G L Sbjct: 27 VQPGEMVALIGASGSGKSTLLRHLAGLACCDSSAGGRIEVLGREVQ--------ATGRLH 78 Query: 344 CPEDRKKEGIIPLGSVGENINISARPS---HSTLGCLLRGDWERGN----ADKQIKSLKV 396 R + I G + + N+ R S + LG L R RG+ +D+Q + Sbjct: 79 GEVRRLRADI---GYIFQQFNLVTRLSVLDNVLLGFLGRMPRWRGSLGMFSDEQKRQAMA 135 Query: 397 KTPTAG------QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQII 450 G Q+ LSGG QQ+ + R L+ +V+L DEP +D + ++ +I+ Sbjct: 136 ALERVGLAERAAQRASTLSGGQQQRVAIARALTQQAEVILADEPIASLDPESARKVMEIL 195 Query: 451 HNL-AADGIAVIVVSSDLMEVMGISDRILVLCEG 483 ++ DG V+V + + R + L G Sbjct: 196 ADINRQDGKTVVVTLHQVDYALRYCSRAVALKGG 229 Lambda K H 0.320 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: 335 Number of extensions: 23 Number of successful extensions: 5 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: 514 Length of database: 276 Length adjustment: 30 Effective length of query: 484 Effective length of database: 246 Effective search space: 119064 Effective search space used: 119064 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: 50 (23.9 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