Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_013011779.1 DACET_RS12695 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::P31373 (394 letters) >NCBI__GCF_000025725.1:WP_013011779.1 Length = 428 Score = 189 bits (479), Expect = 2e-52 Identities = 146/431 (33%), Positives = 214/431 (49%), Gaps = 59/431 (13%) Query: 11 TKAIHAGEHVDVHGSVIEPISLSTT--FKQSS-PANPIGTYE----YSRSQNPNRENLER 63 ++ +H G GS PI +T+ FK S AN G E YSR NP + LE+ Sbjct: 6 SRLLHGGYEPGETGSRAVPIYQTTSYVFKSSEHAANLFGLKEFGNIYSRIMNPTNDVLEK 65 Query: 64 AVAALENAQYGLAFSSGSAT-TATILQSLPQGSHAVSIGDVYGGTHRYFTKVANAHGVET 122 +A LE L+ SSG A T ++L G + V+ +YGGT+ F G+E Sbjct: 66 RLADLEGGTGALSLSSGQAAITFSVLNITAAGQNIVASSSIYGGTYNLFKYTLGRLGIEV 125 Query: 123 SFTNDLLNDLPQLIK---ENTKLVWIETPTNPTLKVTDIQKVADLIKKHAAGQDVILVVD 179 F + D IK ENT+ + E+ NP ++ DI+ ++DL H AG + L+VD Sbjct: 126 RFVDG--TDPESFIKAADENTRAFYTESIGNPAGRLADIRGISDLA--HEAG--IPLIVD 179 Query: 180 NTFLSPYISNPLNFGADIVVHSATKYINGHSDVVLGVLA---------------TNNKPL 224 NT ++PYI P + GADIVV+S TK+I+G+ + G + T P Sbjct: 180 NT-ITPYIFKPFDHGADIVVYSLTKFISGNGTSIGGAVIEKGDFNWANGRYPEITEPDPS 238 Query: 225 YERLQF------------------------LQNAIGAIPSPFDAWLTHRGLKTLHLRVRQ 260 Y L + L +G+ SP+ A GL+TL LR+++ Sbjct: 239 YHGLSYWDAFGNHDKAVLRGASYILKARVQLLRDLGSCLSPYSANQILLGLETLPLRIKK 298 Query: 261 AALSANKIAEFLAADKENVVAVNYPGLKTHPNYDVVLKQHRDALGGGMISFRIKGGAEAA 320 ++ +AEFLA + V VNY GL HP++ + + G +I F IKGG E+ Sbjct: 299 HCENSLTVAEFLAKHPK-VSWVNYAGLSDHPDHKKASEILKHGYGA-IIGFGIKGGLESG 356 Query: 321 SKFASSTRLFTLAESLGGIESLLEVPAVMTHGGIPKEAREASGVFDDLVRISVGIEDTDD 380 KF S ++F+ ++G SL+ PA TH + E R ++GV DD VR+SVGIED D Sbjct: 357 KKFIESVKVFSHLANVGDARSLVIHPASTTHQQLTTEERISAGVTDDYVRLSVGIEDVSD 416 Query: 381 LLEDIKQALKQ 391 L+ D++QAL+Q Sbjct: 417 LIADLEQALEQ 427 Lambda K H 0.315 0.131 0.370 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: 459 Number of extensions: 19 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: 394 Length of database: 428 Length adjustment: 31 Effective length of query: 363 Effective length of database: 397 Effective search space: 144111 Effective search space used: 144111 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 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