Align 2-deoxy-3-keto-D-ribonate cleavage enzyme (characterized)
to candidate Ac3H11_1929 FIG00537796: hypothetical protein
Query= reanno::Burk376:H281DRAFT_00641 (312 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1929 Length = 303 Score = 135 bits (341), Expect = 9e-37 Identities = 99/309 (32%), Positives = 158/309 (51%), Gaps = 28/309 (9%) Query: 4 TSRKVIISCAITGATHVPSMSEFLPITPEQIRDQAIEAAQAGAAIIHLHARDPVDGR--- 60 TS K II+CAITG P +P+TPEQ+ +A A AGAA++H+H R+ G+ Sbjct: 7 TSNKAIITCAITGVLTDPGQHH-VPVTPEQLAKEARGACDAGAAVVHVHFRNQEPGKGHL 65 Query: 61 PTPSPEIFKAFVPAIAEATDAVINITTGGSTRMTLEERLAYPRLARPEMCSLNMGSMNFS 120 P+ P++ + V A+ EA +I T G + L R RPEM + N GS+N+ Sbjct: 66 PSWDPQVARDCVQAMREACPGLIINQTTGVVGPHYQGPLDCLRATRPEMAACNAGSLNY- 124 Query: 121 IHPVAAKI-SSWRYGWEKDYIEGMEDMIFRNTFRDIRNILLELGESGTRFEFECYDVGHL 179 K+ S+ + W M+F N +++ + + E+GT EFEC+DVG + Sbjct: 125 -----LKVRSNGTWAWPP--------MLFDNQPAKVKDFIDVMLETGTLPEFECFDVGIV 171 Query: 180 YNLAHFVDQGLVK---PPFFIQSVFGILGGLGADPENMLLMRSTADRLFGRENYHFSVLG 236 + +V G+ P + V G+ G+ ADP+ + ++ ++ G + +V+G Sbjct: 172 RCVEMYVQTGMYTERLPEY--NFVMGVESGMPADPDLLPILLKL--KIKGAP-WQATVIG 226 Query: 237 AGRHQMPLVTMSAIMGGNVRVGLEDSVYLAKGVKAETNAQQVRKIRRILEELSLEIATPA 296 P+ A +GG++R GLED+ YL G KA++N + K+ E+A+P Sbjct: 227 RSEI-WPVHQRVAELGGHLRTGLEDTFYLPDGTKADSNGPLIEKLAEYARNAGREVASPQ 285 Query: 297 DARKMLGLK 305 +AR MLGLK Sbjct: 286 EARGMLGLK 294 Lambda K H 0.321 0.137 0.400 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: 240 Number of extensions: 17 Number of successful extensions: 5 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: 312 Length of database: 303 Length adjustment: 27 Effective length of query: 285 Effective length of database: 276 Effective search space: 78660 Effective search space used: 78660 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 (21.9 bits) S2: 48 (23.1 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