Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate WP_012116516.1 XAUT_RS23015 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >NCBI__GCF_000017645.1:WP_012116516.1 Length = 398 Score = 320 bits (821), Expect = 3e-92 Identities = 171/387 (44%), Positives = 240/387 (62%), Gaps = 11/387 (2%) Query: 8 TQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFSL 67 T++V++GR K G VN+ + R S+++ + + H G YGRRG T Sbjct: 19 TKVVHSGRDPKRFDGFVNTPVVRGSTVLSATYDDLIHH-----RGRYSYGRRGNPTTEGF 73 Query: 68 QQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLGV 127 + A+ LEGG G L P G +A + S+L+ ++ GDH+LM +TAY P++ FC ++L +LGV Sbjct: 74 ETALRALEGGDGIALTPSGLSACSISLLSVLDAGDHLLMVDTAYRPTRTFCDQVLKRLGV 133 Query: 128 TTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMIDNT 187 T+++DPL+G+ I + ++ NT+ +FLESPGS + E+ DVPAI A R+ +IDNT Sbjct: 134 ETTYYDPLVGSGIAELIRDNTRAIFLESPGSQSFEMQDVPAITAVARA--RGITTLIDNT 191 Query: 188 WAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQMVDAD 247 WA + FK FG+D+SIQA TKY+ GH+D +GT W+++ +G + D Sbjct: 192 WATPLFFKPHAFGVDISIQAGTKYIGGHADLNLGTISAVGPAWKKVIATHGTLGITISPD 251 Query: 248 TAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDFTGS 307 A + +RGLRTL VRL H S L+VA+WL + P+V+RV HPALP GH WKRDFTG+ Sbjct: 252 DAALGARGLRTLAVRLAHHQRSGLEVAQWLQDRPEVSRVLHPALPTDPGHAIWKRDFTGA 311 Query: 308 SGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEIDFS 367 +GLFS +L K++ +A + D +LF M YSWGGYESL + P R D Sbjct: 312 TGLFSLIL-KEVPERAVAAFFDALALFGMGYSWGGYESLAI---PFDCRDYRTATVWDVE 367 Query: 368 GTLIRLHIGLEDVDDLIADLDAGFARI 394 G +RLHIGLEDV DL ADLD FAR+ Sbjct: 368 GPGVRLHIGLEDVADLKADLDQAFARM 394 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: 401 Number of extensions: 19 Number of successful extensions: 5 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