Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate 18081 b4053 alanine racemase (NCBI)
Query= SwissProt::Q88GJ9 (409 letters) >FitnessBrowser__Keio:18081 Length = 359 Score = 110 bits (276), Expect = 5e-29 Identities = 108/352 (30%), Positives = 167/352 (47%), Gaps = 50/352 (14%) Query: 44 AWVEVSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGI---GLVMPSIIAQGVPCVAV 100 A V ++ AL+HN++ L+ ELA SK+ AV+KA+AYGHG+ +P A GV Sbjct: 4 ATVVINRRALRHNLQRLR-ELAPASKMVAVVKANAYGHGLLETARTLPDADAFGV----- 57 Query: 101 ASNEEARVVRASGFTGQLVRVR-------LASLSELEDGLQYDMEELVGSAEFARQADAI 153 A EEA +RA G T ++ + L ++S EE + + E A + + Sbjct: 58 ARLEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHNEEQLAALEEASLDEPV 117 Query: 154 AARHGKTLRIHMALNSSGMSRNGVEMATWSGRGEAL--QITDQKHLKL-VALMTHFAVED 210 + M L++ GM R GV + EA ++T K+++ V +++HFA D Sbjct: 118 T--------VWMKLDT-GMHRLGVRPE----QAEAFYHRLTQCKNVRQPVNIVSHFARAD 164 Query: 211 KDD---VRKGLAAFNEQTDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALF 267 + K LA FN + + A S L P++ D VR G L+ Sbjct: 165 EPKCGATEKQLAIFNTFCEGKPGQRSI---------AASGGILLWPQSHFDWVRPGIILY 215 Query: 268 G------DTVPARTEYKRAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYS 321 G + A + M S + AV + AG VGY T+ RD+RL + +GY Sbjct: 216 GVSPLEDRSTGADFGCQPVMSLTSSLIAVREHKAGEPVGYGGTWVSERDTRLGVVAMGYG 275 Query: 322 DGYRRVFTNKGHVLINGHRVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGK 373 DGY R + VL+NG VP+VG+V+M+ + VD+ K G+ V+L+G+ Sbjct: 276 DGYPRAAPSGTPVLVNGREVPIVGRVAMDMICVDLGPQAQDKAGDPVILWGE 327 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: 316 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: 359 Length adjustment: 30 Effective length of query: 379 Effective length of database: 329 Effective search space: 124691 Effective search space used: 124691 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