Align Lysine racemase; EC 5.1.1.5 (characterized)
to candidate Echvi_1545 Echvi_1545 alanine racemase
Query= SwissProt::M4GGR9 (407 letters) >FitnessBrowser__Cola:Echvi_1545 Length = 384 Score = 153 bits (386), Expect = 9e-42 Identities = 110/380 (28%), Positives = 188/380 (49%), Gaps = 35/380 (9%) Query: 41 NNSWIEISRSALDFNVKKVQSLLGKQSSLCAVLKGDAYGHDLSLVAPIMIENNVKCIGVT 100 + S IEIS+SA N+K ++S +G + + AV+KG+AYGH + + I ++ Sbjct: 3 HTSRIEISKSAYRRNMKFIRSQVGDDTIVSAVIKGNAYGHGIENIIKIAENVGIRHFSAF 62 Query: 101 NNQELKEVRDLGFKGR-LMRVRNATEQEMAQATNYNVEELIGDLDMAKRLDAIAKQQNKV 159 + E K V K +M + Q++ + + + + D +AK+ + Sbjct: 63 STDEAKRVLQASEKNSDIMIMGMVDNQDLEWIIKHRISFFVFEFDRLMAAIKMAKKLHIP 122 Query: 160 IPIHLALNSGGMSRNGLEVDNKSGLEKAKQISQLANLKVVGIMSHYPEEDANKVREDLAR 219 IH+ + +G R G E + K L + +L++ G+ +H+ E +A Sbjct: 123 AKIHVEVETG-FHRTGFEWNEKEFLADVIYEHGI-HLELTGLCTHFAGA------ESIAN 174 Query: 220 FKQQSQQVLEVMGL----ERNNV---TLHMANTFATITVPESWLDMVRVGGIFYGDTIAS 272 + + Q+ + +R+ + T H A + A+++ PE+ +DMVR+G + YG + Sbjct: 175 YLRVQNQIKQYRNFKNWFDRHGIKFGTYHTACSAASLSYPETIMDMVRIGILQYGFWPSQ 234 Query: 273 TDY---------------KRVMTFKSNIASINYYPKGNTVGYDRTYTLKRDSVLANIPVG 317 Y KR++++KS+I SI G+ VGY T+ R +A +PVG Sbjct: 235 ETYMSKFKELAAHRKNPLKRLISWKSSIMSIKEVGMGDFVGYGTTFMAHRPMRIALVPVG 294 Query: 318 YADGYRRVFSNAGHALIAGQRVPVLGKTSMNTVIVDITSLNNIKPGDEVVFFGKQGNSEI 377 Y G+ R+ SN G LI G+ V V+G +MN++ VDIT L ++K GDEVV GKQ N+EI Sbjct: 295 YCHGFSRMLSNLGKVLIQGKMVSVVGTVTMNSISVDITDLKDVKKGDEVVIIGKQKNNEI 354 Query: 378 T----AEEIEDISGALFTEM 393 T +E + ++ L T + Sbjct: 355 TVASFSETTQQVNYELLTRL 374 Lambda K H 0.317 0.133 0.374 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: 356 Number of extensions: 12 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: 407 Length of database: 384 Length adjustment: 31 Effective length of query: 376 Effective length of database: 353 Effective search space: 132728 Effective search space used: 132728 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