Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate YP_426700.1 Rru_A1613 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >NCBI__GCF_000013085.1:YP_426700.1 Length = 392 Score = 331 bits (849), Expect = 2e-95 Identities = 181/393 (46%), Positives = 244/393 (62%), Gaps = 12/393 (3%) Query: 5 KLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVE--AKKHATRNRANGELFYGRRGTL 62 K DT +V++GR + G VN RAS++ F +V +KHA R +YGR GT Sbjct: 2 KQDTTVVHSGRDPQRFDGVVNVPAYRASTVTFPTVADLKRKHAIRFETT---YYGRYGTP 58 Query: 63 THFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKIL 122 T +L++A+ LEG C G AVA ++L F++QGDH+LM +T Y P++ FC L Sbjct: 59 TTAALEEAVAALEGATHCAATSSGMGAVAGALLTFLKQGDHLLMVDTVYWPTRKFCDVFL 118 Query: 123 SKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAII 182 GV T+++DPLIGA I ++PNTKIV+ ESPGS T +V D+PAI + A++ Sbjct: 119 KNFGVETTYYDPLIGAGIAALIRPNTKIVYCESPGSHTFQVQDIPAIAGEAHA--KGALV 176 Query: 183 MIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCW-EQLRENAYLMG 241 ++DNTWA+ + F+ G+DVSIQAATKY+VGHSDAM+GT R W +++ G Sbjct: 177 LLDNTWASPLFFEPFSKGVDVSIQAATKYIVGHSDAMLGTISVRQRDWFLAIKDTLGSFG 236 Query: 242 QMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWK 301 ++ A++ RGLRTL RL +H S+L VA WL P+V RV +PALP GH W Sbjct: 237 YATGSEEAFLGLRGLRTLSARLERHQRSALAVATWLQSQPEVERVLYPALPDDPGHALWT 296 Query: 302 RDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQ 361 RDFTG+SGLF VL K E++A+ LD+ +LF+M YSWGGYESL++ P A R Sbjct: 297 RDFTGASGLFG-VLLKAGTEEQVAHMLDHMTLFAMGYSWGGYESLVI---PTRGAIERTA 352 Query: 362 GEIDFSGTLIRLHIGLEDVDDLIADLDAGFARI 394 + G +RLHIGLED DLIADL AG R+ Sbjct: 353 TQWTHQGPSLRLHIGLEDPADLIADLRAGLDRL 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: 389 Number of extensions: 14 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: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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