Align L-arabinose-binding periplasmic protein; Short=ABP; Flags: Precursor (characterized, see rationale)
to candidate BPHYT_RS19715 BPHYT_RS19715 ATPase
Query= uniprot:B2SYR6 (332 letters) >FitnessBrowser__BFirm:BPHYT_RS19715 Length = 334 Score = 333 bits (855), Expect = 3e-96 Identities = 165/330 (50%), Positives = 224/330 (67%), Gaps = 1/330 (0%) Query: 1 MKRRIFLTLAAAATGVLFNAPVAQAAD-PVKIGFLVKQPEEPWFQDEWKFAEIAAKEKGF 59 ++R +AAAA F ++ AD P+K+GFLVK PE+ WF +E K A ++ GF Sbjct: 5 LRRLTLSAMAAAALAAPFAMQLSAHADAPLKVGFLVKMPEQAWFINEQKAASALGQKDGF 64 Query: 60 TLVKIGAPSGEKVMSAIDNLSAQKAQGFVICTPDVKLGPGIVAKAKADGLKMMTVDDRLV 119 ++V IG P GEKV++AIDNL AQ A+GFVIC PDV+LGP I A+AK +K +TVDD+LV Sbjct: 65 SVVNIGTPDGEKVLAAIDNLGAQGAKGFVICAPDVRLGPAIQARAKRYNMKFVTVDDQLV 124 Query: 120 DGAGKPIASVPHMGISAYNIGKQVGDGLAAEIKKRGWDMKDVGAIDVTYEQLPTAHDRTS 179 D GKP+ +VPH+G+SA+ IG QVG ++ E+K+RGW ++VGA+ +T +LPTA RT Sbjct: 125 DSTGKPLPNVPHLGMSAFKIGNQVGTAISEEMKRRGWKPEEVGALRITNYELPTAKLRTD 184 Query: 180 GATDALIAAGFPKANIVMAPQAKTDTENAFNAANIALTKNPQFKHWVAYALNDEGVLGAV 239 GAT +L+A GF K NI APQ TD E FNA++ L ++P K WV +ALN+E VLG V Sbjct: 185 GATQSLLAGGFKKENIFDAPQKTTDDEGGFNASSPVLAQHPNIKKWVIFALNEESVLGGV 244 Query: 240 RAAEGRGFKADNMIGIGIGGSDSALNEFKKPSPTGFYGTVIISPKRHGEETSTLMYDWIT 299 RA E A ++IG+GI G+ A EF+K PTGFYGT+ +S HG+E++ + +WI Sbjct: 245 RATEQLHIPAADVIGVGINGAGEAFAEFQKKEPTGFYGTIAVSSTMHGKESTENLVEWIK 304 Query: 300 QGKAPPPLTLTTGMLATRDNVADVRQKMGL 329 GK PP T TTG L R N DVR+++G+ Sbjct: 305 DGKQPPADTQTTGKLMVRSNWQDVRKELGI 334 Lambda K H 0.316 0.133 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: 358 Number of extensions: 17 Number of successful extensions: 1 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: 332 Length of database: 334 Length adjustment: 28 Effective length of query: 304 Effective length of database: 306 Effective search space: 93024 Effective search space used: 93024 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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