Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate 7023484 Shewana3_0714 alanine racemase (RefSeq)
Query= SwissProt::Q88GJ9 (409 letters) >FitnessBrowser__ANA3:7023484 Length = 358 Score = 114 bits (284), Expect = 6e-30 Identities = 114/365 (31%), Positives = 178/365 (48%), Gaps = 39/365 (10%) Query: 47 EVSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSI-IAQGVPCVAVASNEE 105 E+S+SALQ+N+ L+ + A +S++ AV+KA+ YGHG+ V + A G +A EE Sbjct: 8 EISSSALQNNLAVLRQQ-ASRSQVMAVVKANGYGHGLLNVANCLHTADGF---GLARLEE 63 Query: 106 ARVVRASGFTGQLVRVR-LASLSELEDGLQYDMEELV---GSAEFARQADAIAARHGKTL 161 A +RA G +L+ + ++L + +D++ +V E QA K + Sbjct: 64 ALELRAGGVKARLLLLEGFFRSTDLPLLVAHDIDTVVHHESQIEMLEQATL-----SKPV 118 Query: 162 RIHMALNSSGMSRNGVEMATWSGRGEALQITDQKHLKLVALMTHFAVEDKDD---VRKGL 218 + + ++S GM R GV ++ L D K + LMTHFA D+ + + + Sbjct: 119 TVWLKVDS-GMHRLGVTPEQFTQVYARLMACDNV-AKPIHLMTHFACADEPENHYTQVQM 176 Query: 219 AAFNEQTDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFGDT-----VPA 273 FN+ T L L ANS L P+++ D +R G AL+G + A Sbjct: 177 QTFNQLTADLPGFRTL---------ANSAGALYWPKSQGDWIRPGIALYGVSPVTGDCGA 227 Query: 274 RTEYKRAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKGH 333 AM S + AV + AG VGY +T +D+RL + +GY DGY R Sbjct: 228 NHGLIPAMNLVSRLIAVRDHKAGQPVGYGCYWTAKQDTRLGVVAIGYGDGYPRNAPEGTP 287 Query: 334 VLINGHRVPVVGKVSMNTLMVDV-TDFPDVKGGNEVVLFGKQAGGEITQAEMEEINGALL 392 V +NG RVP+VG+VSM+ L VD+ D D+ G+E +L+ G + E+ E G + Sbjct: 288 VWVNGRRVPIVGRVSMDMLTVDLGADATDLV-GDEALLW----GAALPVEEVAEHIGTIA 342 Query: 393 ADLYT 397 +L T Sbjct: 343 YELVT 347 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: 311 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: 409 Length of database: 358 Length adjustment: 30 Effective length of query: 379 Effective length of database: 328 Effective search space: 124312 Effective search space used: 124312 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