GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Methanosarcina acetivorans C2A

Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_011022927.1 MA_RS15665 anthranilate synthase component I

Query= BRENDA::P9WFX1
         (450 letters)



>NCBI__GCF_000007345.1:WP_011022927.1
          Length = 560

 Score =  142 bits (359), Expect = 2e-38
 Identities = 94/277 (33%), Positives = 137/277 (49%), Gaps = 3/277 (1%)

Query: 167 TGVREVPQSRSVDVSDDPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAID-FPLTYR 225
           +G  + P S     S D SGF   V  A + I AG   +V+LSR  E       F L  +
Sbjct: 274 SGPAKAPNSNVQVCSVDRSGFEESVLQAKEHIFAGDIFQVVLSRKCEFKMEQSPFELYIQ 333

Query: 226 LGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLAR 285
           L R  N     ++ + G +  +G SPE +  V    V+I  P+AGT   G+  A D    
Sbjct: 334 L-RAINPSPYMYIFEFGDLAIVGASPETLLTVHKRTVIIN-PIAGTCPRGKSEAEDETLA 391

Query: 286 DDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDP 345
             + ++ KE  EH + V     ++  ++E GS  V  FM V +   VQH+ ST+   L P
Sbjct: 392 SHMLNDEKERAEHVMLVDLGRNDVRMVSESGSVKVSGFMKVLKYSHVQHIESTVSGTLRP 451

Query: 346 SSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLR 405
             D+  A  A+FPA T SG PK   +E I   +  PRG+Y G V   S +G  D A+ +R
Sbjct: 452 ECDQFDAFRAVFPAGTLSGAPKIRAMEIISEREAVPRGIYGGGVGYYSWNGDADFAIVIR 511

Query: 406 AAYQVGGRTWLRAGAGIIEESEPEREFEETCEKLSTL 442
                G +  ++AGAGI+ +S+P  EF ET  K++ +
Sbjct: 512 TLLIQGRKASVQAGAGIVADSDPAYEFRETDRKMAAM 548


Lambda     K      H
   0.319    0.135    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: 466
Number of extensions: 17
Number of successful extensions: 3
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: 450
Length of database: 560
Length adjustment: 34
Effective length of query: 416
Effective length of database: 526
Effective search space:   218816
Effective search space used:   218816
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: 52 (24.6 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