Align cysteine-S-conjugate beta-lyase (EC 4.4.1.13); alanine racemase (EC 5.1.1.1); glutamate racemase (EC 5.1.1.3) (characterized)
to candidate WP_085771337.1 B1812_RS09255 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q9X0Z7 (379 letters) >NCBI__GCF_002117405.1:WP_085771337.1 Length = 438 Score = 167 bits (424), Expect = 4e-46 Identities = 120/408 (29%), Positives = 199/408 (48%), Gaps = 47/408 (11%) Query: 14 DIPLKALSFPIFETTNFYFDSFDEMSKALRNGDYE-FVYKRGSNPTTRLVEKKLAALEEC 72 D KA++ PI++T + FDS D AL N + E + Y R +NPTT ++E+++AALE Sbjct: 15 DPATKAIAVPIYQTVAYEFDSADH-GAALFNLEAEGYRYSRIANPTTSVLERRIAALEGG 73 Query: 73 EDARLVASGMSAISLSILHFLSSGDHVVCVDEAYSWAKKFFNYLSKKFDIEVSYVPPDAE 132 A VASG +A+ + + +G ++V Y ++ + + + P DA Sbjct: 74 VGALCVASGQAALHYAFANLADAGGNIVSTPTLYGTTHTLLQHVLPRQGVTARFAPTDAP 133 Query: 133 R-IVEAITKKTKLIYLESPTSMRMKVIDIRKVTEAAGELKIKTVIDNTWASPIFQKPKLL 191 + I EAI + T+ ++ ES + + DI E+A I ++DNT +PI +P Sbjct: 134 QDIAEAIDENTRAVFCESVGNPAGNICDIAAFAESAHARGIPLIVDNTVPTPILLRPIEH 193 Query: 192 GVDVVVHSATKYISGHGDVMAGVIA---------------------------------GD 218 G D+VVHS TK+I GHG + G I GD Sbjct: 194 GADIVVHSLTKFIGGHGTTLGGAIVDSGRFPWAKHPTRFPMFNEPDESYHGLVYVERFGD 253 Query: 219 VEDMKNIFVDEYKNIGPVLSPIEAWLILRGLRTLELRMKKHYENALVVSDFLMDHPKVLE 278 ++ + G V++P A+L+L+GL TL LR+++H ENA V++FL ++ Sbjct: 254 SAYLERARSVYLRTTGAVMAPFSAFLLLQGLETLALRVERHVENARKVAEFLHQDRRIAW 313 Query: 279 VNYPMNPRSPQYELASSQMSG-GSGLMSFRLKTDSAEKVKEFVESLRVFRMAVSWGSHEN 337 VNY P + Y+ + G +++F ++ E+ K F +SL++ + V+ G ++ Sbjct: 314 VNYAGFPDNAYYDRVKKYLGGRAPSVLTFGVE-GGFERTKTFYDSLKLLKRLVNIGDAKS 372 Query: 338 LVV-------PRVAYGDCPKKDV--NLIRIHVGLGDPEKLVEDLDQAL 376 L +++ + V +LIR+ VGL E ++EDLDQAL Sbjct: 373 LATHPASTTHRQMSLEGLKRAGVSPDLIRLSVGLEHYEDIIEDLDQAL 420 Lambda K H 0.318 0.136 0.391 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: 358 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 379 Length of database: 438 Length adjustment: 31 Effective length of query: 348 Effective length of database: 407 Effective search space: 141636 Effective search space used: 141636 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 (21.7 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