Align Uncharacterized protein (characterized, see rationale)
to candidate Ac3H11_2337 hypothetical protein, not 6-phosphogluconolactonase
Query= uniprot:Q881W7 (359 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2337 Length = 391 Score = 226 bits (576), Expect = 8e-64 Identities = 129/357 (36%), Positives = 198/357 (55%), Gaps = 22/357 (6%) Query: 3 AATFAYISSPADGLISQYRLDEQSGALSLVEQTKAGDQVNPMAISPDGKALFAALRSKPY 62 AAT+ Y+S+ +S + LD +GAL V+ T G PMA+SPD K L+ ALRS+P+ Sbjct: 55 AATWVYVSNADSQDVSVFELDRNAGALKPVDTTALGGMAMPMAVSPDKKVLYVALRSQPF 114 Query: 63 QVLSFSIEPATGHLKPLSQAPLAESLAYLSTDRSGRFLFGASYGADLLSVQPIDAQHRPS 122 +V+S +I+PA+G L+ L +APLA+S+A + TD +GR+LF ASY ++V I Sbjct: 115 RVVSLAIDPASGKLRKLGEAPLADSMANIDTDATGRWLFAASYPGHKITVNSIGKDGAVG 174 Query: 123 DSIETYKTGMHAHSVRTDPSNRFVYAGNLGVDRVLQYRLEPKDGKLVPIGEGFVAV-PDN 181 + T HAH++ D +NR V A +LG D + +R + + GKL V P+ Sbjct: 175 AVQQLIPTAPHAHAIHADAANRHVLATSLGGDNLSAWRFDAETGKLTAHEPALTTVTPEK 234 Query: 182 TGPRHLAFSSDGRFLYVVGEMSGTVTAFLINEKTGALKQVSQADGIPARLKLAPGQARDA 241 +GPRH + R LY++ E+ +V +++ G L+ V +A +PA P Sbjct: 235 SGPRHFVWDKAQRSLYLLNELDASVHVMAYDKERGTLRAVQRATTLPAGFAGKP------ 288 Query: 242 RNNDLKDDPTPRIWAADIRLAPDGKWLFISERTTSSVSVFKVDPAKGNVTFVENYPVEEK 301 WAADI L+PDG+ L+ SERT+S++S F+VD A G + + P EK Sbjct: 289 -------------WAADIHLSPDGRTLYASERTSSTLSSFRVDAATGQLQPLGQVPT-EK 334 Query: 302 QPRNIAVSPNGRWLLVSGEKSDKVGSYAIG-ASGALKRVSEAPSGKGALWIEMLSQP 357 PR AV +GR+L+ +G++S V + I A+G + P+GK W+E++ P Sbjct: 335 TPRGFAVDSSGRFLIAAGQESHHVALHPIDPATGIPGAATRVPAGKNPNWVEIVDLP 391 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: 450 Number of extensions: 29 Number of successful extensions: 15 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: 391 Length adjustment: 30 Effective length of query: 329 Effective length of database: 361 Effective search space: 118769 Effective search space used: 118769 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: 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