Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate WP_068464132.1 APY04_RS14670 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >NCBI__GCF_001541235.1:WP_068464132.1 Length = 395 Score = 332 bits (852), Expect = 9e-96 Identities = 177/387 (45%), Positives = 249/387 (64%), Gaps = 11/387 (2%) Query: 8 TQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFSL 67 T+ V++GR+ G VN + R S+++F +VE K R++A YGR T T SL Sbjct: 15 TRAVHSGRAPHDNFGFVNPPVYRGSTVLFPTVE--KLWNRDQA---YTYGRTCTPTVKSL 69 Query: 68 QQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLGV 127 Q A+ ++EGGA L G AV+ +ILAF++ GDH+LM + Y+P++ FC +L++LGV Sbjct: 70 QDAIADIEGGATTELTASGYQAVSTAILAFVKAGDHILMVDNVYQPTRKFCDYLLARLGV 129 Query: 128 TTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMIDNT 187 T+++DPLIGA I ++PNT+++F ESPGS T EV D+PAI R D +++DNT Sbjct: 130 ETTYYDPLIGAGIADLIRPNTRLIFTESPGSQTFEVQDIPAIARVARE--RDLWLLMDNT 187 Query: 188 WAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQMVDAD 247 WA+ + F+ + G+DVSIQAATKY+VGH+DAM+G CN R + + +G ++ Sbjct: 188 WASPLYFRPFEHGVDVSIQAATKYIVGHADAMLGAITCNERAAKYIAMAKDQLGVCPGSE 247 Query: 248 TAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDFTGS 307 ++ RGLRTL RL QHH + L++A WL P+VARV HPAL HE WKRDF G+ Sbjct: 248 ETFLGMRGLRTLPTRLAQHHRAGLEIARWLEGRPEVARVLHPALESHPQHELWKRDFLGA 307 Query: 308 SGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEIDFS 367 SGLF VL K ++++ +A LD LF M +SWGGYESL++ P + R + Sbjct: 308 SGLFGVVL-KPVSDKAVAAMLDGLELFGMGFSWGGYESLVI---PFDARSYRTATDWQPE 363 Query: 368 GTLIRLHIGLEDVDDLIADLDAGFARI 394 G +RLHIGLEDV+DL ADL+AGF R+ Sbjct: 364 GPTLRLHIGLEDVNDLRADLEAGFERL 390 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: 399 Number of extensions: 14 Number of successful extensions: 4 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: 395 Length adjustment: 31 Effective length of query: 364 Effective length of database: 364 Effective search space: 132496 Effective search space used: 132496 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