Align Uncharacterized protein (characterized, see rationale)
to candidate Ac3H11_3954 hypothetical protein, not 6-phosphogluconolactonase
Query= uniprot:Q881W7 (359 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3954 Length = 343 Score = 212 bits (539), Expect = 1e-59 Identities = 128/362 (35%), Positives = 191/362 (52%), Gaps = 24/362 (6%) Query: 1 MQAATFAYISSPADGLISQYRLDEQSGALSLVEQTKAGDQVNPMAISPDGKALFAALRSK 60 M T ++S G + L ++G L + G Q+ PMA+SPDGK L+ A RS Sbjct: 1 MDNDTLVFVSCADSGELHVLHLSSETGLLRTEQVLALGGQLMPMALSPDGKRLYVARRSD 60 Query: 61 PYQVLSFSIEPATGHLKPLSQAPLAESLAYLSTDRSGRFLFGASYGADLLSVQPI--DAQ 118 P V++ +++ G + L +A L S+A+++TD +GR+L ASYGADL++VQ I D Sbjct: 61 PLAVVTLAVDARAGRAEVLGEAALPASMAHVATDGTGRWLLSASYGADLVAVQAIAADGV 120 Query: 119 HRPSDSIETYKTGMHAHSVRTDPSNRFVYAGNLGVDRVLQYRLEPKDGKLVPIGEGFVAV 178 TY TG HAHS P NRFV A +LG ++ +YR + G L P A+ Sbjct: 121 VAAGRGATTYATGRHAHSALASPGNRFVLAASLGGGQLHRYRFDAATGALQPTDPAVFAL 180 Query: 179 PDNTGPRHLAFSSDGRFLYVVGEMSGTVTAFLINEKTGALKQVSQADGIPARLKLAPGQA 238 P TGPRHL F++ G +Y++GE+ V +E +G L+ + +P PG Sbjct: 181 PAGTGPRHLRFNARGDRIYLLGELDACVHVLGWDEASGGLELLQSLPTLP------PGST 234 Query: 239 RDARNNDLKDDPTPRIWAADIRLAPDGKWLFISERTTSSVSVFKVDPAKGNVTFVENYPV 298 A W AD+ L+ DG WL+ SER + +++ F VD G + ++ Y Sbjct: 235 GPA-------------WGADLHLSADGHWLYTSERNSHTLAGFAVDAVTGRLAPID-YWS 280 Query: 299 EEKQPRNIAVSPNGRWLLVSGEKSDKVGSYAIG-ASGALKRVSEAPSGKGALWIEML-SQ 356 + QPR ++P+GR L+ +G+ S +VG + I SGAL +V+E G WI +L Q Sbjct: 281 TQLQPRGFVITPDGRHLIAAGQISHRVGVHLIAPGSGALTQVAEHDVGLNPNWITVLPMQ 340 Query: 357 PD 358 PD Sbjct: 341 PD 342 Lambda K H 0.314 0.132 0.383 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: 439 Number of extensions: 26 Number of successful extensions: 11 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: 359 Length of database: 343 Length adjustment: 29 Effective length of query: 330 Effective length of database: 314 Effective search space: 103620 Effective search space used: 103620 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: 42 (22.0 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