GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Lentibacillus jeotgali Grbi

Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_010529287.1 ON01_RS01750 anthranilate synthase component I

Query= BRENDA::P9WFX1
         (450 letters)



>NCBI__GCF_000224785.1:WP_010529287.1
          Length = 467

 Score =  122 bits (307), Expect = 2e-32
 Identities = 85/261 (32%), Positives = 129/261 (49%), Gaps = 3/261 (1%)

Query: 183 DPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLG 242
           D   F   V +A D I  G  ++V+LS+ ++     D    YR  R+ N     F +   
Sbjct: 199 DKQHFMHNVEIAKDHIKNGDIYQVVLSQRMKAAMQGDPFTFYRKLRKVNPSPYMFYINFD 258

Query: 243 GIRALGYSPE-LVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAIS 301
               LG SPE L+     D  ++T P+AGTR  G     D   R++L ++ KEI EH + 
Sbjct: 259 DYVVLGASPESLIETSGRD--IMTNPIAGTRPRGSTTDGDGALRNELLTDEKEISEHRML 316

Query: 302 VRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVT 361
           V  S  ++  + E  S +V  +M V     V H+ S +  +L      + AL A  PA T
Sbjct: 317 VDLSRNDLGRVCEIDSVSVPTYMKVENYQHVMHMVSEVHGKLAEGFTSIDALIACLPAGT 376

Query: 362 ASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAG 421
            SG PK   ++ I  L++  RG Y+G V  +S +  L+ AL +R+        +L+AGAG
Sbjct: 377 VSGAPKIRAMQIINDLEKVKRGAYAGGVGYISFNDNLNIALAIRSLIVKENFAYLQAGAG 436

Query: 422 IIEESEPEREFEETCEKLSTL 442
           I+ +S+PE E+ ET  K  +L
Sbjct: 437 IVYDSDPETEYNETLHKARSL 457


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: 386
Number of extensions: 13
Number of successful extensions: 1
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: 467
Length adjustment: 33
Effective length of query: 417
Effective length of database: 434
Effective search space:   180978
Effective search space used:   180978
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: 51 (24.3 bits)

This GapMind analysis is from Jul 26 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