GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Sulfurimonas denitrificans DSM 1251

Align Cystathionine beta-lyase, chloroplastic; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_011372397.1 SUDEN_RS04000 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase

Query= SwissProt::P53780
         (464 letters)



>NCBI__GCF_000012965.1:WP_011372397.1
          Length = 421

 Score =  200 bits (508), Expect = 9e-56
 Identities = 126/407 (30%), Positives = 208/407 (51%), Gaps = 46/407 (11%)

Query: 99  DPFDAMSTPLYQTATFKQPS--------AIENGPYDYTRSGNPTRDALESLLAKLDKADR 150
           D    M+ P+YQT  ++  S        +++     YTR  NPT D  E   A L+  + 
Sbjct: 15  DSQGTMAVPIYQTTAYEFNSVEHAADLFSLKQLGNIYTRLNNPTTDVFEKRFASLEGGEA 74

Query: 151 AFCFTSGMAA-LSAVTHLIKNGEEIVAGDDVYGGSDRLLSQVVPRSGVVVKRVNTTKLDE 209
           A   +SGM+A   A+ +    GE IV    +YGGS  L +  + R G+  +  +   +  
Sbjct: 75  ALATSSGMSATFFAIVNATAAGENIVCAKQLYGGSLTLNTHTLKRFGIEARYFDVHDMSS 134

Query: 210 VAAAIGPQTKLVWLESPTNPRQQISDIRKISEMAHAQGALVLVDNSIMSPVLSRPLELGA 269
           + + I  +T++++ ES TNP   ++DI  I+++A   G L +VDN++ +PVL RP E GA
Sbjct: 135 LESLIDDKTRVIFFESLTNPSIDVADIEAITKIADKYGILSVVDNTVATPVLCRPFEFGA 194

Query: 270 DIVMHSATKFIAGHSDVMAGVLAVKG---EKLAKEVYF---------------------- 304
           DIV+HSA+K+  G    + G+L  +    EKL     +                      
Sbjct: 195 DIVVHSASKYTTGQGLAIGGILVERKNLVEKLRSNPRYEHFNNPDPSYHGLIYVNIGLPP 254

Query: 305 --------LQNSEGSGLAPFDCWLCLRGIKTMALRIEKQQENARKIAMYLSSHPRVKKVY 356
                   L    G+ L+PF+ WL ++GI+T++LR+++  +NA  +A +L SHP+VKKV 
Sbjct: 255 FTLRARLSLSRDLGAVLSPFNSWLFIQGIETLSLRMKEHSKNALALAEFLESHPKVKKVN 314

Query: 357 YAGLPDHPGH---HLHFSQAKGAGSVFSFITGSVALSKHLVETTKYFSIAVSFGSVKSLI 413
           Y GL  +  +     +F   + +G + SF   S+  +  +V+ TK +S+ V+ G  KS+I
Sbjct: 315 YPGLKSNANYKNAQKYFDGGECSG-LLSFEVASLQEATKIVDATKLYSLVVNIGDSKSII 373

Query: 414 SMPCFMSHASIPAEVREARGLTEDLVRISAGIEDVDDLISDLDIAFK 460
           + P   +H  +  +   A G+   L+RIS G+E + DLI D+  A +
Sbjct: 374 THPASTTHQQLNEQELIACGVPSGLIRISCGLESIKDLIDDMKQALE 420


Lambda     K      H
   0.316    0.130    0.369 

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: 405
Number of extensions: 14
Number of successful extensions: 4
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: 464
Length of database: 421
Length adjustment: 32
Effective length of query: 432
Effective length of database: 389
Effective search space:   168048
Effective search space used:   168048
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: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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