GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Rhodospirillum rubrum ATCC 11170

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_011390962.1 RRU_RS16580 O-succinylhomoserine sulfhydrylase

Query= BRENDA::Q5H4T8
         (397 letters)



>NCBI__GCF_000013085.1:WP_011390962.1
          Length = 413

 Score =  242 bits (617), Expect = 2e-68
 Identities = 141/357 (39%), Positives = 208/357 (58%), Gaps = 4/357 (1%)

Query: 39  IYATSTYAQSS-PGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAA-TSTVM 96
           +Y  +  A+++  G  + + YSR  NPT   +E  +AALEG     A ASGMAA TS ++
Sbjct: 54  VYPNAEEAEAAFDGTLERYVYSRFRNPTISVFEERLAALEGAPVCKATASGMAAVTSALL 113

Query: 97  ELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIE 156
             + AG  VVA  DL+G    +   +  +  G+   FVD  +  A+  A+   T+ V++E
Sbjct: 114 CQVRAGDRVVAARDLFGSCSWVIGDLLAQY-GVSAEFVDTENLDAWAQALAKPTRAVFLE 172

Query: 157 TPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHS 216
           TP+NP L++VD+  +  +A   G   VVDN FA+P+LQRP   GAD+VVHSATK+++G  
Sbjct: 173 TPSNPTLRIVDLKGVCDLAHAAGATVVVDNAFATPLLQRPRDFGADVVVHSATKWIDGQG 232

Query: 217 DMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALA 276
             +GG AV+ D A     +       G    PF++++ L+GL+TL LR+  H   AL LA
Sbjct: 233 RCLGG-AVLCDEAFNETYLGPFLRHTGPCLAPFNAWVMLKGLETLSLRINRHSATALTLA 291

Query: 277 QWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTL 336
             +E HPA+ + +YPGLASHP+H LA+ QM   GG++++ LKGG  +A RF     +  +
Sbjct: 292 GLIEGHPAVARALYPGLASHPRHALAQSQMKAGGGVIALSLKGGRASAYRFLNALSIVDI 351

Query: 337 AESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393
           + +LG  +SL  HP   TH  +    +   GI + L+R SVG+ED  DL  D+  AL
Sbjct: 352 SNNLGDAKSLACHPWTTTHQRLSPEEKLIQGIDEGLIRFSVGLEDPEDLAADIGAAL 408


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: 468
Number of extensions: 16
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: 397
Length of database: 413
Length adjustment: 31
Effective length of query: 366
Effective length of database: 382
Effective search space:   139812
Effective search space used:   139812
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.

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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