Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate 5210851 Shew_3277 alanine racemase (RefSeq)
Query= SwissProt::Q88GJ9 (409 letters) >FitnessBrowser__PV4:5210851 Length = 358 Score = 117 bits (293), Expect = 5e-31 Identities = 110/358 (30%), Positives = 177/358 (49%), Gaps = 25/358 (6%) Query: 47 EVSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAVASNEEA 106 E+S AL+ N++ L+ +LA +SK+ AV+KA+ YGHG+ V + + +A EEA Sbjct: 8 EISGDALKANLKRLR-QLAPQSKVMAVVKANGYGHGLLNVAHCLAS--ADGFGLARLEEA 64 Query: 107 RVVRASGFTGQLVRVR-LASLSELEDGLQYDMEELVGSAEFARQADAIAARHGKTLRIHM 165 +RA G + +L+ + S++ +++D++ +V +A A K + + M Sbjct: 65 LELRAGGVSAKLLLLEGFFRPSDVATLVEHDIDTVVHHESQLEMLEA--ASLAKPVTVWM 122 Query: 166 ALNSSGMSRNGVEMATWSGRGEALQITDQKHLKLVALMTHFAVEDKDDVRKGLAAFNEQT 225 +++ GM R G + + + LQ K + LMTHFA D+ D A + Sbjct: 123 KIDT-GMHRLGFNLDQFEAIYQRLQACANV-AKPINLMTHFACADEPD-NPATAEQARRF 179 Query: 226 DWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFGDTVPARTEYKR------ 279 + + + DR+ ANS ATL + D +R G AL+G + P + R Sbjct: 180 EQMTANLPGDRT-----LANSAATLYWQATQADWIRPGIALYGVS-PVVGDLGRNHGLEP 233 Query: 280 AMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKGHVLINGH 339 AM+ S + AV + AG+ VGY + +D++L + +GY DGY R V +NG Sbjct: 234 AMELVSQLIAVRDHKAGDPVGYGSYWRAKQDTKLGVVAIGYGDGYPRNAPEGTPVWVNGR 293 Query: 340 RVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGKQAGGEITQAEMEEINGALLADLYT 397 VPVVG+VSM+ L VD+ K G+ VL+GK E E+ E G + +L T Sbjct: 294 LVPVVGRVSMDMLTVDLGLDATDKVGDTAVLWGKALPVE----EVAEHIGTIAYELVT 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: 301 Number of extensions: 24 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