Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate WP_084200507.1 C0029_RS02215 alanine racemase
Query= SwissProt::Q88GJ9 (409 letters) >NCBI__GCF_002869505.1:WP_084200507.1 Length = 360 Score = 128 bits (321), Expect = 3e-34 Identities = 111/341 (32%), Positives = 170/341 (49%), Gaps = 31/341 (9%) Query: 52 ALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAVASNEEARVVRA 111 AL+HN+ ++ G +C V+KA+ YGHG GL + + +AVA EEA +R Sbjct: 12 ALRHNLAHARSLAPGARTMC-VVKANGYGHG-GLAIAQALEAHTDALAVACIEEALELRE 69 Query: 112 SGFTGQLVRVR-LASLSELEDGLQYDMEELVGS---AEFARQADAIAARHGKTLRIHMAL 167 G ++ + + + EL ++++ ++ + ++ QA +AA L++ Sbjct: 70 GGVRCPILLLEGVFAADELPLAAEHNLWVMIDNHKQLQWLEQAQ-LAAPITCWLKV---- 124 Query: 168 NSSGMSRNGVEMATWSGRGEALQITDQKHLKLVALMTHFAVED---KDDVRKGLAAFNEQ 224 +GM R GV+ L + +LV THFA D D + + FN Sbjct: 125 -DTGMHRLGVQPEEAEAFHSRLMACANRTGELVTC-THFASADDLSSDQTARQIELFNAI 182 Query: 225 TDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFGDT----VPARTEYKR- 279 T A L + AANS L P++ D +R G L+G++ A TE R Sbjct: 183 T------ASLPGPR---SAANSPGLLGWPDSHFDWIRPGYMLYGNSPFAQAHANTEALRP 233 Query: 280 AMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKGHVLINGH 339 M S V ++ G++VGY T+T R SR+A I++GY DGY R+ N VLING Sbjct: 234 VMTLTSAVISLRDLAPGDSVGYAATWTAERPSRIATISIGYGDGYPRLANNGTPVLINGQ 293 Query: 340 RVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGKQ-AGGEI 379 RVP+VG+VSM+ + VDVTD +V G+E +L+G Q GE+ Sbjct: 294 RVPLVGRVSMDMITVDVTDLSEVAIGDEAILWGPQLTAGEV 334 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: 344 Number of extensions: 11 Number of successful extensions: 2 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: 360 Length adjustment: 30 Effective length of query: 379 Effective length of database: 330 Effective search space: 125070 Effective search space used: 125070 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 24 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