Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate Echvi_3728 Echvi_3728 3-carboxymuconate cyclase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314 (389 letters) >FitnessBrowser__Cola:Echvi_3728 Length = 392 Score = 220 bits (561), Expect = 5e-62 Identities = 132/353 (37%), Positives = 194/353 (54%), Gaps = 13/353 (3%) Query: 30 VGSYTAGQSQGIYRLAFDSRTGQIDASPLQVIKSANPSWLTLSKDQRHLFVVNENGPGQT 89 +G+YT+ S G + + + T D S L NPS++ + + +F V E G G+ Sbjct: 43 LGTYTSKPSDGFHLIQYHPETSTFD-SVLMESDINNPSFVISNLKRDLVFTVQEEG-GEN 100 Query: 90 DPVGRVSSFAIDPKTHALSLISQVQSLGNEPTHSSLSIDGSHLFVSNYSVAEDPGGTLAV 149 G V SF D ++L +S S G+ P + +LS D +F NY G LAV Sbjct: 101 G--GSVCSFRFDRSANSLKKLSTSASQGSGPCYITLSPDEKFIFAGNYG-----SGDLAV 153 Query: 150 LPVAADGKLKAVVQMSSHPASRVNPERQASAHVHSTIPSPDGRYVFANDLGADKVFAYRF 209 LP+ DG L VQ H S VN RQ+S HVHS + P+G+ +F DLG DKV Y + Sbjct: 154 LPINEDGTLGEAVQTIQHTGSSVNEGRQSSPHVHSLVFHPNGKQLFVADLGTDKVSIYNY 213 Query: 210 DPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGKHAWLTMEMSAQVAVFDYHDGQLEQ 269 DP PLT ++PA + GSGPRHL F+ G +L E++++V ++DY+ + + Sbjct: 214 DPDRKE--PLTASSPASFTVKAGSGPRHLAFNQSGDKIYLIHEITSEVGLYDYNLDENKI 271 Query: 270 TQMVDLAAGQP--VSDKAAAALHASADGKFLYVSNRGTANQLLVFAIDPATGHLSELQRR 327 T + A +K AA + S DG+FLY SNRG +N+++VF+I+ TG L ++Q Sbjct: 272 THLDSYALTPQGFEGEKGAAEIKISDDGQFLYASNRGDSNEIIVFSINAQTGTLDKIQAI 331 Query: 328 AVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDARTGLLGKTVQKLPMDAP 380 + G PR F+L P G FL + NQ S+ I+ ER+ R+G++ KT KLP+ P Sbjct: 332 SSGGKTPRNFALSPDGTFLFVGNQNSDSILAYERNPRSGIIKKTNAKLPIHRP 384 Score = 29.6 bits (65), Expect = 2e-04 Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 7/83 (8%) Query: 4 LWPLLMAGSIGAMGVQVASAEDYQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQVIKS 63 L P G GA ++++ +D Q L S G S I + +++TG +D +Q I S Sbjct: 279 LTPQGFEGEKGAAEIKIS--DDGQFLYAS-NRGDSNEIIVFSINAQTGTLDK--IQAISS 333 Query: 64 AN--PSWLTLSKDQRHLFVVNEN 84 P LS D LFV N+N Sbjct: 334 GGKTPRNFALSPDGTFLFVGNQN 356 Lambda K H 0.316 0.132 0.382 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: 428 Number of extensions: 30 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 389 Length of database: 392 Length adjustment: 31 Effective length of query: 358 Effective length of database: 361 Effective search space: 129238 Effective search space used: 129238 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: 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