Align Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 (characterized)
to candidate AZOBR_RS08350 AZOBR_RS08350 alanine racemase
Query= SwissProt::Q88GJ9 (409 letters) >FitnessBrowser__azobra:AZOBR_RS08350 Length = 378 Score = 116 bits (291), Expect = 1e-30 Identities = 111/369 (30%), Positives = 163/369 (44%), Gaps = 35/369 (9%) Query: 42 SNAWVEVSASALQHNIRTLQAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAVA 101 + A + + A+ N L+ +A ++ AV+KA+AYG G+G V+P++ A G VA Sbjct: 13 AGAVLTIDLGAVVANWTQLRDRVA-PAECAAVVKANAYGLGVGRVVPALAAAGCRTFVVA 71 Query: 102 SNEEARVVRASGFTGQLVRVRLASLSELEDGLQYD---------MEELVGSAEFARQADA 152 EEA VRA T R+ SL L G D + L A + A A Sbjct: 72 QFEEALAVRAVAPTN----ARVLSLGGLPAGTAPDFTAQRILPVLNHLGDIAAWQAHARA 127 Query: 153 IAARHGKTLRIHMALNSSGMSRNGVEMATWSGRGEALQITDQKHLKLVALMTHFAVEDKD 212 + I +N G+ + E+ T G L+ D + MTH A D+D Sbjct: 128 QGTALPAVVHIDTGMNRLGLGPD--ELDTLVGDLSRLEGVDVR-----VWMTHLACADED 180 Query: 213 DVRKGLAAFNEQTDWLIKHA--RLDRSKLTLHAANSFATLEVPEARLDMVRTGGALFG-- 268 V N Q + A RL ++ + ANS D+VR G AL+G Sbjct: 181 SV------MNSQQLGRFRSAIGRLPAAEASF--ANSSGIFHGTAFHFDLVRPGCALYGVN 232 Query: 269 DTVPARTEYKRAMQFKSHVAAVHSYPAGNTVGYDRTFTLARDSRLANITVGYSDGYRRVF 328 T A + ++ + + V + + TVGY T +A ++A I VGY+DGY R Sbjct: 233 PTPAAENPMRGTIRLDARLLQVRNVDSPMTVGYGATHRVAARGKIATIAVGYADGYLRSL 292 Query: 329 TNKGHVLINGHRVPVVGKVSMNTLMVDVTDFPD--VKGGNEVVLFGKQAGGEITQAEMEE 386 + +GHV +NG PVVG+VSM+ + VDV+ PD V G V L G + +E Sbjct: 293 SGRGHVFVNGVAAPVVGRVSMDLVTVDVSHLPDAAVTPGGLVELIGPNRPVDTVASEGGT 352 Query: 387 INGALLADL 395 I +L L Sbjct: 353 IGYEILTSL 361 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: 354 Number of extensions: 21 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: 378 Length adjustment: 31 Effective length of query: 378 Effective length of database: 347 Effective search space: 131166 Effective search space used: 131166 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