Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate PP_5269 PP_5269 alanine racemase, PLP-binding
Query= SwissProt::Q88GJ9 (409 letters) >FitnessBrowser__Putida:PP_5269 Length = 357 Score = 122 bits (306), Expect = 2e-32 Identities = 113/337 (33%), Positives = 162/337 (48%), Gaps = 28/337 (8%) Query: 48 VSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAVASNEEAR 107 + AL+HN R L EL G +K AV+KADAYGHG ++ A+ AVA EEA Sbjct: 8 IDLQALRHNYR-LARELTG-AKALAVIKADAYGHGAVRCALALEAEA-DGFAVACIEEAL 64 Query: 108 VVRASGFTGQLVRVR-LASLSELEDGLQYDMEELVGSAEFARQADAIAARH-GKTLRIHM 165 +RA+G ++ + SEL ++D+ +V S Q +AI K L + + Sbjct: 65 ELRAAGIKAPVLLLEGFFEASELALIAEHDLWCVVHSLW---QLEAIEKTPLHKPLNVWL 121 Query: 166 ALNSSGMSRNGVEMATWSGRGEALQITDQKHLKLVALMTHFAVEDK---DDVRKGLAAFN 222 L+S GM R G+ + + L + + + + LMTHFA D+ D + +A F Sbjct: 122 KLDS-GMHRVGLHPKDYHDAYQRLLASGK--VSRIVLMTHFARADELDADATSQQIAVFE 178 Query: 223 EQTDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFGDTV--PARTEYKR- 279 L L NS L P+A D VR G L+G T A+ E R Sbjct: 179 AARQGLAAECSL---------RNSPGVLGWPQAPSDWVRPGLMLYGATPFEVAQAEAARL 229 Query: 280 --AMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKGHVLIN 337 M +S V +V PAG VGY F R +R+ + +GY+DGY R N VL+ Sbjct: 230 QPVMTLQSRVISVRELPAGEPVGYGAKFVSPRPTRVGVVAMGYADGYPRQAPNGTPVLVA 289 Query: 338 GHRVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGKQ 374 G R ++G+VSM+ L +D+TD P G+ V +GKQ Sbjct: 290 GKRTQLIGRVSMDMLSIDLTDVPQATVGSPVEFWGKQ 326 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: 15 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: 357 Length adjustment: 30 Effective length of query: 379 Effective length of database: 327 Effective search space: 123933 Effective search space used: 123933 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