Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate WP_092483985.1 BM299_RS11030 alanine racemase
Query= SwissProt::Q88GJ9 (409 letters) >NCBI__GCF_900115975.1:WP_092483985.1 Length = 380 Score = 191 bits (484), Expect = 4e-53 Identities = 126/366 (34%), Positives = 189/366 (51%), Gaps = 12/366 (3%) Query: 41 NSNAWVEVSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAV 100 N+ W E++ +A+ HNIR L+ ++L AV+KA+AYGHG G V + G + V Sbjct: 4 NTPVWSEINLAAIAHNIRQLKNITRPDAELMAVVKANAYGHGAGQVARVAMENGATRLGV 63 Query: 101 ASNEEARVVRASGFTGQLVRVRLASLSELEDGLQYDMEELVGSAEFARQADAIAARHGKT 160 A E +R +G L+ + + L D+ + V S AR+ A AAR GK Sbjct: 64 ARVSEGEALRRAGIDAPLLILGYTVPEDYPSLLANDLAQTVYSLAAARELSATAARAGKK 123 Query: 161 LRIHMALNSSGMSRNGV---EMATWSGRGEALQITDQKHLKLVALMTHFAVEDKDDVRKG 217 +H+ +++ GM R G + A E I HL++ + THFA D D Sbjct: 124 AVVHIKVDT-GMGRLGFCIDKEAVKEAVREITAIAKLPHLEVEGIYTHFAAADSRDKSYT 182 Query: 218 LAAFNEQTDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFG-----DTVP 272 + + + + L +R + L HAANS A +++PE LD+VR G A++G + + Sbjct: 183 IKQWRKFNELLEALSREGLAFLYRHAANSAALIDLPETHLDLVRAGIAIYGVYPSNEVLT 242 Query: 273 ARTEYKRAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKG 332 R K AM K+ VA V PAG + Y T +D+ +A I GY+DGY R+ +++G Sbjct: 243 ERVSLKPAMAVKARVAHVKRVPAGTGISYGVTHITPKDTLVATIPAGYADGYSRLLSSRG 302 Query: 333 HVLINGHRVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGKQAGGEITQAEMEEINGALL 392 VL+ G R PV+G+V M+ MVDV DV+ G EVVL G+Q G ++ A +EI G + Sbjct: 303 EVLLRGRRAPVIGRVCMDQFMVDVGHLSDVEPGEEVVLMGRQ-GDDMVSA--DEIAGKIG 359 Query: 393 ADLYTV 398 Y V Sbjct: 360 TIAYEV 365 Lambda K H 0.318 0.132 0.377 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: 321 Number of extensions: 18 Number of successful extensions: 3 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: 409 Length of database: 380 Length adjustment: 31 Effective length of query: 378 Effective length of database: 349 Effective search space: 131922 Effective search space used: 131922 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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