GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Nocardiopsis lucentensis DSM 44048

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_017597122.1 D471_RS0102240 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q5H4T8
         (397 letters)



>NCBI__GCF_000341125.1:WP_017597122.1
          Length = 390

 Score =  302 bits (773), Expect = 1e-86
 Identities = 168/354 (47%), Positives = 220/354 (62%), Gaps = 4/354 (1%)

Query: 42  TSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLD 100
           T T A S  G    F Y+R  NPT  A E  VA LEGG  A A  SGM A T+T+  LL 
Sbjct: 38  TETMAASFQGAGSPFVYARYGNPTVAALEDAVADLEGGAGAIASGSGMGAITATLWALLG 97

Query: 101 AGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTN 160
            G HVVA + LYGGT  L   +R R  G++ + VD  DPAA  AA+R DT+++ +ET  N
Sbjct: 98  TGGHVVAQERLYGGTQALLTTLRERW-GVEVTQVDAGDPAAVDAALRPDTRVLVLETIAN 156

Query: 161 PMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVG 220
           P  ++ D+ A+  +AR+HG   +VDNTFA+P+L RP+  GAD+VVHSATKY+ GHSD +G
Sbjct: 157 PTGQVADLPALTALARRHGTTVIVDNTFATPLLCRPIEHGADIVVHSATKYMGGHSDTIG 216

Query: 221 GIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLE 280
           G+AV  D   L  ++    N  G V  PF ++L  RGL TL +RMR HC NA  LA+ L+
Sbjct: 217 GVAVFADAGTLT-RVRERTNEFGAVMEPFAAWLINRGLSTLGVRMRRHCANAEELARRLD 275

Query: 281 THPAIEKVIYPGLASHPQHVLAKRQM-SGFGGIVSIVLKGGFDAAKRFCEKTELFTLAES 339
            HPA+ +V Y GL  HP H  A+  +  GFGG+++  L GG +A + F E+  L  LA S
Sbjct: 276 RHPAVTRVHYAGLPDHPGHATARELLDGGFGGVLAFELAGGLEAGRSFAERVRLAVLAPS 335

Query: 340 LGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393
           LG V +LV HPA  +H  +      + G+S+ L+RLS GIED+ DL  DLERAL
Sbjct: 336 LGDVRTLVMHPASTSHRMLDAEGLARAGVSEGLIRLSAGIEDVEDLWADLERAL 389


Lambda     K      H
   0.320    0.134    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: 519
Number of extensions: 34
Number of successful extensions: 5
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: 397
Length of database: 390
Length adjustment: 31
Effective length of query: 366
Effective length of database: 359
Effective search space:   131394
Effective search space used:   131394
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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