Align L-arabinose-binding periplasmic protein; ABP (characterized)
to candidate BPHYT_RS19715 BPHYT_RS19715 ATPase
Query= SwissProt::P02924 (329 letters) >FitnessBrowser__BFirm:BPHYT_RS19715 Length = 334 Score = 283 bits (725), Expect = 3e-81 Identities = 149/324 (45%), Positives = 211/324 (65%), Gaps = 5/324 (1%) Query: 7 ALAAIGLAA--VMSQSAMAEN-LKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAV 63 A+AA LAA M SA A+ LK+GFLVK PE+ WF E K A G+ GF V+ I Sbjct: 12 AMAAAALAAPFAMQLSAHADAPLKVGFLVKMPEQAWFINEQKAASALGQKDGFSVVNIGT 71 Query: 64 PDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPM 123 PDGEK L AID+L A GAKGFVIC PD +LG AI A+A+ Y+MK + VDDQ V++ GKP+ Sbjct: 72 PDGEKVLAAIDNLGAQGAKGFVICAPDVRLGPAIQARAKRYNMKFVTVDDQLVDSTGKPL 131 Query: 124 DTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALK 183 VP + M+A KIG + G + +EM++RGW +E + IT EL TA+ RT G+ +L Sbjct: 132 PNVPHLGMSAFKIGNQVGTAISEEMKRRGWKPEEVGALRITNYELPTAKLRTDGATQSLL 191 Query: 184 AAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQG 243 A GF ++ I+ P K+ D G F+A++ +L QHP +K W+I +N+ +VLGGVRATE Sbjct: 192 AGGFKKENIFDAPQKTTDDEGGFNASSPVLAQHPNIKKWVIFALNEESVLGGVRATEQLH 251 Query: 244 FKAADIIGIGINGV-DAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPK 302 AAD+IG+GING +A +E K + TGFYG++ S +HG +S+E L W+ +PP Sbjct: 252 IPAADVIGVGINGAGEAFAEFQKKEPTGFYGTIAVSSTMHGKESTENLVEWIKDGKQPPA 311 Query: 303 FTEVTDVVLITRDNFKEELEKKGL 326 T+ T +++ R N+++ ++ G+ Sbjct: 312 DTQTTGKLMV-RSNWQDVRKELGI 334 Lambda K H 0.315 0.132 0.381 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: 320 Number of extensions: 9 Number of successful extensions: 2 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: 329 Length of database: 334 Length adjustment: 28 Effective length of query: 301 Effective length of database: 306 Effective search space: 92106 Effective search space used: 92106 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