Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate WP_011383705.1 AMB_RS06585 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >NCBI__GCF_000009985.1:WP_011383705.1 Length = 390 Score = 320 bits (820), Expect = 4e-92 Identities = 174/392 (44%), Positives = 243/392 (61%), Gaps = 10/392 (2%) Query: 5 KLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTH 64 K T++++AGR + GAVN + AS+++ SV A + + + G + YGR GT T Sbjct: 2 KKSTRILHAGRKPEAFHGAVNPPVYHASTILHPSVAAMEKSGKTPFEG-VRYGRFGTPTT 60 Query: 65 FSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSK 124 F+L++A+ ELEGG V G AA+ ++LAF++ GDH+LM +T Y P++ FC +L Sbjct: 61 FALEEAVAELEGGHRTVATSSGLAAITGALLAFLKAGDHLLMVDTTYFPTRKFCDSVLGG 120 Query: 125 LGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMI 184 LG+ T+++DPL+GA I ++PNT++VF ESPGS+T EV D+PAI A + A++M+ Sbjct: 121 LGIETTYYDPLVGAGITALMRPNTRVVFTESPGSLTFEVQDIPAIAEAAHA--GGAVVMM 178 Query: 185 DNTWAAGVL-FKALDFGIDVSIQAATKYLVGHSDAMIGT-AVCNARCWEQLRENAYLMGQ 242 DNTW GVL F+ GID+SIQAATKY+VGH+DAM+GT W Q++ + G Sbjct: 179 DNTW--GVLHFQPFTKGIDISIQAATKYIVGHADAMLGTITAATPELWLQVKTSLAAFGA 236 Query: 243 MVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKR 302 + Y+ RGLRTL VRLRQH ES+L++ WL P+V RV +P L GHE WKR Sbjct: 237 SPGTEEMYLGLRGLRTLPVRLRQHAESALRLTRWLEARPEVDRVLYPPLASDPGHELWKR 296 Query: 303 DFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQG 362 DFTG GLF +L K + + LD +S F + +SWGG+ESL++ I IR Sbjct: 297 DFTGGCGLFGVIL-KPASKAAVDAMLDGYSHFKLGFSWGGFESLVIPTSGHSI--IRTAT 353 Query: 363 EIDFSGTLIRLHIGLEDVDDLIADLDAGFARI 394 G +R H GLED DDL DL+ GF R+ Sbjct: 354 PWTPVGPSLRFHAGLEDADDLEEDLERGFERL 385 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: 404 Number of extensions: 21 Number of successful extensions: 7 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: 390 Length adjustment: 31 Effective length of query: 364 Effective length of database: 359 Effective search space: 130676 Effective search space used: 130676 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 09 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