Align cystathionine gamma-lyase; EC 4.4.1.1 (characterized)
to candidate RR42_RS32610 RR42_RS32610 O-acetylhomoserine aminocarboxypropyltransferase
Query= CharProtDB::CH_122519 (419 letters) >FitnessBrowser__Cup4G11:RR42_RS32610 Length = 424 Score = 234 bits (598), Expect = 3e-66 Identities = 151/425 (35%), Positives = 223/425 (52%), Gaps = 47/425 (11%) Query: 29 TLAVHAGAPHDPTTGAVIAPISLSTTFAQESVGKPVGLYE-------YTRSSNPNRDNFE 81 T+AVH G DPTT AV PI + +A ++ L++ Y+R NP D E Sbjct: 5 TIAVHGGYSPDPTTRAVAVPIYQTVAYAFDNAQHGADLFDLKVPGNIYSRIMNPTNDVLE 64 Query: 82 EAVASLEHAKYALAFSSGSATTATILHSLAP-GSHVVSVSDVYGGTHRYFTKVAAAHGVN 140 + +A+LE ALA +SG A + ++A G +++S S +YGGT+ F G+ Sbjct: 65 QRLAALEGGVGALALASGMAAITYAIQTIAEAGDNIISASQLYGGTYNLFAHTLPLSGIE 124 Query: 141 VSFSSCLELDVEKLIRPNETKLVWIETPSNPTLALVDIRKVAAVAHRHGVLVVVDNTFMS 200 F+ + TK +++E+ NP +VDI +A VAH HG+ ++VDNT S Sbjct: 125 TRFADGRNPAAFGDLVDARTKAIFVESVGNPLGNIVDIEAIAKVAHSHGIPLIVDNTVPS 184 Query: 201 PYVQNPLDHGADVVIHSVTKYINGHSDVLMGV----AAFNSDELKERFTFLQNA------ 250 PY+ P +HGAD+V+HS+TKY+ GH + + G F E K RF L Sbjct: 185 PYLCRPFEHGADIVVHSLTKYLGGHGNSVGGAIVDSGKFPWAEHKARFKRLNEPDVSYHG 244 Query: 251 -----------------------IGAVPSPFDCWLAHRGLKTLHLRAREATANATAVALA 287 GA SPF+ +L +G++TL LR T NA AVA Sbjct: 245 VVYTEALGAAAYIGRARVVPLRNTGAALSPFNAFLILQGIETLALRLDRITENALAVARH 304 Query: 288 LESSPHVISVNYPGLNSHPNREIAVKQHRKGMGGGMLSFRIK-GGHKAAHLFCEYTKIFT 346 L++SP V VN+ GL HP+ + V+++ G G G+LSF +K GG +A F + ++FT Sbjct: 305 LKASPKVEWVNFAGLPEHPDHAL-VQRYLGGRGPGILSFGLKSGGREAGARFLDALQLFT 363 Query: 347 LAESLGGVESLCEVPSSMTHAGIPKEEREAAGVYDDLVRMSCGIEDVEDLTADTMQALER 406 ++G +SL P+S TH + E +AAGV +D+VR+S GIE ++DL D LER Sbjct: 364 RLVNIGDAKSLATHPASTTHRQLDAAELKAAGVSEDMVRLSIGIEHIDDLLED----LER 419 Query: 407 AVAAS 411 A+AA+ Sbjct: 420 ALAAA 424 Lambda K H 0.316 0.130 0.377 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: 515 Number of extensions: 27 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: 419 Length of database: 424 Length adjustment: 32 Effective length of query: 387 Effective length of database: 392 Effective search space: 151704 Effective search space used: 151704 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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