Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate WP_083441487.1 NITAL_RS11785 hypothetical protein
Query= BRENDA::A0PKT3 (388 letters) >NCBI__GCF_000969705.1:WP_083441487.1 Length = 578 Score = 221 bits (563), Expect = 4e-62 Identities = 144/389 (37%), Positives = 213/389 (54%), Gaps = 19/389 (4%) Query: 13 GLATRAIHSGYRPDPATGAVNAPIYASSTFA---QDGVGGLR----GGYEYARTGNPTRT 65 G ATRA+H P V+ PI+ S+T+ VG L GY Y R NPT T Sbjct: 187 GFATRAVHGATVPPVGQHPVSVPIHPSATWGTATSAEVGDLLTDEVAGYVYGRYDNPTST 246 Query: 66 ALEAALAAVEDAAFGRAFSSGMAAADCALRAMLRPGDHVVIPDDAYGGTFRLIDKVF--T 123 AL A + ++ +A + +SG AA L +LR V+ YGGT+ L+ ++ Sbjct: 247 ALHAVIGSLHEAPAAWSAASGTAAIHAVLD-VLRGEGRVLATAMLYGGTWALLRRLERDA 305 Query: 124 GWNVEYTPV-ALADLDAVRAAIRPTTRLIWVETPTNPLLSIADIAGIAQLGADSSAKVLV 182 GW V++ P+ ADL RAA+ ++ VET NP +IADI IA + + +++V Sbjct: 306 GWKVDHAPLLTAADL---RAALTDEHTVVHVETIANPSTAIADIPAIAAVCQERGVELVV 362 Query: 183 DNTFASPALQQPLSLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDQSFAFLQNGAGAV 242 DNTFASP L +P++LGA V+ S TK++GGH DVV G + +DE + + + G++ Sbjct: 363 DNTFASPVLCRPVTLGATAVVESATKFLGGHGDVVAGVVAGSDELVGRVREHVYELGGSL 422 Query: 243 PGPFDAYLTMRGLKTLVLRMQRHSENAAAVAEFLAEHP-AISTVLYPGLPSHPGHAVAAR 301 GPF+A+L +RG++TL LR+++ S NA AVA LA P + V +P L +HP HA+ Sbjct: 423 -GPFEAWLVVRGIQTLALRVRQASANATAVAAELAAAPRGVVAVHHPSLDAHPQHAMVPT 481 Query: 302 QMRGFGGMVSVRMRAGRTAAEQLCAKTNIFILAESLGSVESLIEHPSAMTHASTAGSQLE 361 + G G + R AAE +F+ A SLG SL+ HP++ +H +L Sbjct: 482 MLSGLPGALLAVDLGSRPAAEAFADACRVFVRAASLGGTHSLVLHPASTSHRQLRDDELR 541 Query: 362 VP---DDLVRLSVGIEDVADLLDDLKQAL 387 + VRLSVG+E+ DL+ D++ AL Sbjct: 542 LAGLGPGTVRLSVGVEETEDLVADVRHAL 570 Lambda K H 0.318 0.133 0.386 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: 684 Number of extensions: 36 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: 388 Length of database: 578 Length adjustment: 33 Effective length of query: 355 Effective length of database: 545 Effective search space: 193475 Effective search space used: 193475 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: 51 (24.3 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