Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate RR42_RS34985 RR42_RS34985 mandelate racemase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__Cup4G11:RR42_RS34985 Length = 368 Score = 146 bits (368), Expect = 1e-39 Identities = 118/372 (31%), Positives = 168/372 (45%), Gaps = 29/372 (7%) Query: 1 MKITAVRTHLLEHRLD--TPFESASMRFDRRAHVLVEIECDDGTVGWGECL----GPARP 54 M T V+ LL+ L P A F + +V I CDDG G G G + Sbjct: 1 MSATIVQVELLQVDLPPRVPRSDAIQSFVMQETPMVRIRCDDGAEGTGYAYTIGTGGSSV 60 Query: 55 NAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKHYG 114 A + + LIG+DP Q E IW L A ++ AL+ ID ALWD + + G Sbjct: 61 MALLRDHLAPRLIGRDPAQIEAIWRELLFATHATSVGAITSLALAAIDTALWDWRCRRDG 120 Query: 115 ASISMLLGGRWRESVRAYAT-GSFKRDNVDRVSDNASEMAERRAEGFHACKIKIGFG-VE 172 + + GG + V Y T G + + D + SE R GF K+K+G Sbjct: 121 QPLWLAAGGA-QPRVPVYTTEGGWLHLDADTL---VSEAVAAREAGFRGAKLKVGRARAS 176 Query: 173 EDLRVIAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYA 232 ED+ +AAVR+A+G LM+DAN +T EAI A GI WFEEP+ + + + Sbjct: 177 EDVARLAAVRDAVGDGFELMVDANQCFTAAEAIRRAPHYAELGIAWFEEPLPADDIGGHV 236 Query: 233 RVRAGQPIPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVR 292 R+ A +P+A GE+ + + + GA I+Q D+ GG + K+A LA H + Sbjct: 237 RLAASTSVPIAVGESLYSPGQFAEYVRQGACGIVQADVARIGGITPWLKVAHLAEAHNLS 296 Query: 293 IVPHVWGTGVQIAAALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGV 352 I PH +++ +L A P+ V I + E A +EA G Sbjct: 297 ICPHFL---MELHVSL---CAAVPNAAWVEYIPQLDEI---------AASSVRIEA--GH 339 Query: 353 VTIPDGPGLGIE 364 PD PGLGIE Sbjct: 340 AIAPDAPGLGIE 351 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: 415 Number of extensions: 21 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: 368 Length adjustment: 30 Effective length of query: 348 Effective length of database: 338 Effective search space: 117624 Effective search space used: 117624 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