Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_028586001.1 G494_RS0120435 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q96VU7 (417 letters) >NCBI__GCF_000429965.1:WP_028586001.1 Length = 427 Score = 191 bits (486), Expect = 3e-53 Identities = 139/418 (33%), Positives = 204/418 (48%), Gaps = 42/418 (10%) Query: 21 GFGTLAVHAGSPHDPATGAVIEAISLSTTFA----QTAVG----KPVGEFEYSRSSNPNR 72 GF T +HAG DPATG+ I +T++A Q A K G Y+R NP Sbjct: 9 GFNTRQLHAGQVADPATGSRAVPIYQTTSYAFKDSQHAADLFALKEAGNI-YTRIMNPTT 67 Query: 73 ANFEKMVAALEHAKYALAYSSG-SATTANILQSLAAGSHVISVSDVYGGTHRYFTQVAKA 131 E+ +A LE ALA SSG A L G H++S + +YGGT+ Sbjct: 68 DVLEQRLADLEGGVGALAASSGHGAQVMAFLTICGQGDHIVSSNSLYGGTYTQLQYTLPR 127 Query: 132 HGVKVTFT-PEIEVDIRDHITDATKLVWIETPSNPTLRLVDIRAVATAAHERGILVVVDN 190 G+ V+F P I TKL++ ET NP L + VA A I +V+DN Sbjct: 128 LGITVSFADPRDPESFARAIQPNTKLIYGETLGNPALTVFPFEEVAAIAAAVQIPLVIDN 187 Query: 191 TFLSPYVQNPLDHGADIVVHSVTKYINGHSDVVMG--------------VAAFNSDE--- 233 T +PY+ PL+ GA+IV HS TK++NGH + + G +++F + Sbjct: 188 TLATPYLCRPLEWGANIVSHSTTKFLNGHGNSIGGILVDGGNFDWQSGKISSFTEPDPSY 247 Query: 234 ---LYARL---SFLQNA-------IGAVPSAFDSWLAHRGAKTLHLRAREATTNATAIAH 280 +YA L +F+ A IG + F+SWL +G +TL LR NA A Sbjct: 248 HGLIYAELGAPAFILKARVQVLRDIGVSQAPFNSWLTVQGIETLSLRMERHVANALETAR 307 Query: 281 ALEASPLVISVNYPGLESHPHRAIALKQHRNGMGGGMLSFRIHGGHAAAEKFCQYTKIFT 340 LE V V+YPGL SHP A + G G +++F I GG A +F + ++F+ Sbjct: 308 FLEGHARVSWVSYPGLSSHPDHGRACRYLPQG-AGAVIAFGIQGGVEAGRRFIDHLQLFS 366 Query: 341 LAESLGGVESLCEIPSSMTHAGIPKAQREAVGIFDDLVRISCGVEDAEDLKADVLQAL 398 ++G +SL P+S TH+ + A+ G+ ++++R+S G+ED ED+ D+ QAL Sbjct: 367 HVANVGDAKSLAIHPASTTHSQLSPAELLEAGVQEEMIRLSIGLEDLEDIFWDLDQAL 424 Lambda K H 0.317 0.130 0.378 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: 508 Number of extensions: 26 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: 417 Length of database: 427 Length adjustment: 32 Effective length of query: 385 Effective length of database: 395 Effective search space: 152075 Effective search space used: 152075 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 (21.7 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