Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate WP_012049960.1 SWIT_RS19075 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >NCBI__GCF_000016765.1:WP_012049960.1 Length = 398 Score = 362 bits (929), Expect = e-104 Identities = 197/390 (50%), Positives = 255/390 (65%), Gaps = 8/390 (2%) Query: 5 KLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTH 64 K T+LV AGR K G VN + RAS+++FDSV + R +G L+YGRRGT T Sbjct: 10 KPGTRLVTAGRHAKNRRGIVNPPVWRASTILFDSVAELRAGVRKPDDG-LYYGRRGTPTQ 68 Query: 65 FSLQQAMCELE-GGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILS 123 +SL +A+ ELE G AG VL+P G AA++ +L+ + GD +LM ++AYEPS+ C+ +L Sbjct: 69 WSLAEALTELEPGAAGTVLYPSGVAAISAVLLSLLAPGDELLMVDSAYEPSRAICNGLLR 128 Query: 124 KLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIM 183 + G+ T ++DP IGA I + T++VFLESPGS+T EV DVPAI AA R+ + Sbjct: 129 RFGIETRFYDPAIGAGIADLIGDRTRVVFLESPGSLTFEVQDVPAIAAAARA--RGVTTV 186 Query: 184 IDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQM 243 +DNTWA +LF AL G+D+SI A TKY+VGHSD M+G+A +E+LR ++ +GQ Sbjct: 187 LDNTWATPLLFPALAHGVDISILACTKYIVGHSDVMMGSATAVPGHFEKLRRTSHALGQC 246 Query: 244 VDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRD 303 V D AY+ +RGLRTL +RLRQH E +L VA WLAE PQVARV HPALP GHE WKRD Sbjct: 247 VSPDDAYLAARGLRTLQLRLRQHEEGALAVARWLAEQPQVARVLHPALPDCPGHELWKRD 306 Query: 304 FTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGE 363 F+G+SGLFS VL ++ A +D LF + +SWGGYESL L P A +R Sbjct: 307 FSGASGLFSIVLDGG-DDAARAALIDGLDLFGIGFSWGGYESLALPVDP---AGLRTATS 362 Query: 364 IDFSGTLIRLHIGLEDVDDLIADLDAGFAR 393 G IRLHIG+ED DLIADL G AR Sbjct: 363 WQAEGPAIRLHIGIEDPADLIADLGRGLAR 392 Lambda K H 0.321 0.135 0.402 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: 455 Number of extensions: 21 Number of successful extensions: 6 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: 395 Length of database: 398 Length adjustment: 31 Effective length of query: 364 Effective length of database: 367 Effective search space: 133588 Effective search space used: 133588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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