Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate 6938959 Sama_3057 alanine racemase (RefSeq)
Query= SwissProt::Q88GJ9 (409 letters) >FitnessBrowser__SB2B:6938959 Length = 364 Score = 131 bits (330), Expect = 3e-35 Identities = 115/365 (31%), Positives = 182/365 (49%), Gaps = 33/365 (9%) Query: 47 EVSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQG-----VPCVAVA 101 E+S+ AL+ N++ L+ ++A SK+ AV+KA+ YGHG+ L + ++ +A Sbjct: 8 EISSRALKANLKRLR-QIAPGSKVMAVVKANGYGHGL-LNVAEVLTDAHSNADADGFGLA 65 Query: 102 SNEEARVVRASGFTGQLVRVRLASLSE-LEDGLQYDMEELVGSAEFARQADAIAARHGKT 160 EEA VRA G + +L+ + SE L +++D++ +V ++++ T Sbjct: 66 RLEEALEVRAGGVSARLLLLEGFFRSEDLPLLVEHDIDTVVHHVSQLDMLESVSLSKPVT 125 Query: 161 LRIHMALNSSGMSRNGVEMATWSGRGEALQITDQKHLKLVALMTHFAVED---KDDVRKG 217 + + + SGM R G + + + LQ + K V LMTHF+ D KD Sbjct: 126 VWLKI---DSGMHRLGFHASEFKDVYQRLQ-QNPNVAKPVHLMTHFSCADEPQKDFTATQ 181 Query: 218 LAAFNEQTDWLIKHARLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFGDTVPA---- 273 +A FN T L L ANS L P+++ D +R G AL+G + A Sbjct: 182 MAHFNALTQGLPGDRTL---------ANSAGVLYWPQSQADWIRPGIALYGVSPVAGDLG 232 Query: 274 -RTEYKRAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVFTNKG 332 + AM+ S + AV + AG +VGY +T +RD+RL + +GY DGY R Sbjct: 233 SNHGLEPAMELVSQLIAVREHSAGESVGYGAYWTASRDTRLGVVAIGYGDGYPRNAPEGT 292 Query: 333 HVLINGHRVPVVGKVSMNTLMVDVTDFPDVKGGNEVVLFGKQAGGEITQAEMEEINGALL 392 VL+NG RVP+VG+VSM+ L VD+ K G+ +L+GK E+ E+ E G + Sbjct: 293 PVLVNGRRVPIVGRVSMDMLTVDLGPDAADKVGDRALLWGK----ELPVEEVAERIGTIA 348 Query: 393 ADLYT 397 +L T Sbjct: 349 YELVT 353 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: 327 Number of extensions: 26 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: 364 Length adjustment: 30 Effective length of query: 379 Effective length of database: 334 Effective search space: 126586 Effective search space used: 126586 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