Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate 1937093 b4478 galactonate dehydratase (NCBI)
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__Keio:1937093 Length = 382 Score = 152 bits (384), Expect = 1e-41 Identities = 122/394 (30%), Positives = 181/394 (45%), Gaps = 45/394 (11%) Query: 1 MKITAVRTHLLEHRLDTPFESASMRFDRRAHVLVEIECDDGTVGWGECL--GPARPNAAV 58 MKIT + T+ L R + ++IE D+G VGWGE + G AR A Sbjct: 1 MKITKITTYRLPPRW----------------MFLKIETDEGVVGWGEPVIEGRARTVEAA 44 Query: 59 VQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKHYGASIS 118 V +LIGQDP + +W V+Y A +G L ++A++GID ALWDIKGK A + Sbjct: 45 VHELGDYLIGQDPSRINDLWQVMYRAGFYRGGPIL-MSAIAGIDQALWDIKGKVLNAPVW 103 Query: 119 MLLGGRWRESVRAYA-TGSFKRDNVDRVSDNASEMAERRAEGFHACKI----KIGF---- 169 L+GG R+ ++AY+ G DR +D + R GF K+ ++G Sbjct: 104 QLMGGLVRDKIKAYSWVGG------DRPADVIDGIKTLREIGFDTFKLNGCEELGLIDNS 157 Query: 170 -GVEEDLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQL 228 V+ + +A +REA G + +D + + A L + + EEPV+ EQ Sbjct: 158 RAVDAAVNTVAQIREAFGNQIEFGLDFHGRVSAPMAKVLIKELEPYRPLFIEEPVLAEQA 217 Query: 229 DAYARVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATL 288 + Y ++ A IP+A GE R+ + L AG + ILQPDL GG +E KIA +A Sbjct: 218 EYYPKLAAQTHIPLAAGERMFSRFDFKRVLEAGGISILQPDLSHAGGITECYKIAGMAEA 277 Query: 289 HGVRIVPHVWGTGVQIAAALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQAV----LRE 344 + V + PH + +AA L D V N + +N + + +E Sbjct: 278 YDVTLAPHCPLGPIALAACLHI------DFVSYNAVLQEQSMGIHYNKGAELLDFVKNKE 331 Query: 345 PLEAVNGVVTIPDGPGLGIEINRDALTEFRMPDP 378 V G PGLG+EI+ + EF P Sbjct: 332 DFSMVGGFFKPLTKPGLGVEIDEAKVIEFSKNAP 365 Lambda K H 0.321 0.138 0.431 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: 396 Number of extensions: 18 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: 378 Length of database: 382 Length adjustment: 30 Effective length of query: 348 Effective length of database: 352 Effective search space: 122496 Effective search space used: 122496 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: 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