Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate H281DRAFT_00589 H281DRAFT_00589 alanine racemase
Query= SwissProt::Q88GJ9 (409 letters) >FitnessBrowser__Burk376:H281DRAFT_00589 Length = 356 Score = 117 bits (293), Expect = 5e-31 Identities = 106/337 (31%), Positives = 156/337 (46%), Gaps = 33/337 (9%) Query: 48 VSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAVASNEEAR 107 + SAL +N+ + A KSK+ AV+KA+AYGHG+ P + A + EEA Sbjct: 9 IHTSALANNLAVAR-RYAPKSKIWAVVKANAYGHGLARAFPGLRA--TDGFGLLDLEEAV 65 Query: 108 VVRASGFTGQLVRVR-LASLSELEDGLQYDMEELVGSAEFARQADAIAARHGKTLRIHMA 166 +R G+ G ++ + ++++ +Y + + S E R + AR K + I + Sbjct: 66 KLRELGWAGPILLLEGFFRPTDIDVIDRYSLTTALHSDEQLRMLEM--ARLSKPVNIQLK 123 Query: 167 LNSSGMSRNGVE----MATWSGRGEALQITDQKHLKLVALMTHFAVEDKD-DVRKGLAAF 221 +NS GM+R G A W R A Q Q + LMTHF+ D + V + AF Sbjct: 124 MNS-GMNRLGYTPEKFRAAWE-RARACQGVGQ-----ITLMTHFSDADSERGVAHQMEAF 176 Query: 222 NEQTDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFGDTVPAR------T 275 + L ANS ATL P++ D VR G L+G + T Sbjct: 177 ERGAQGIAGMRSL---------ANSAATLWHPQSHFDWVRPGIILYGASPSGMSAAIQGT 227 Query: 276 EYKRAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKGHVL 335 + AM S + AV + G+TVGY F R+ + GY+DGY RV V+ Sbjct: 228 GLQPAMTLTSELIAVQNIAEGHTVGYGSLFKARGPMRIGVVACGYADGYPRVAPEGTPVI 287 Query: 336 INGHRVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFG 372 + G R VVG+VSM+ L VD+T P G+ V L+G Sbjct: 288 VEGVRTRVVGRVSMDMLTVDLTPVPTANVGSRVELWG 324 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: 309 Number of extensions: 11 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: 356 Length adjustment: 30 Effective length of query: 379 Effective length of database: 326 Effective search space: 123554 Effective search space used: 123554 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 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