GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Pseudomonas simiae WCS417

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate GFF1850 PS417_09410 isopropylmalate isomerase

Query= curated2:O27668
         (428 letters)



>FitnessBrowser__WCS417:GFF1850
          Length = 472

 Score =  218 bits (555), Expect = 3e-61
 Identities = 147/438 (33%), Positives = 212/438 (48%), Gaps = 58/438 (13%)

Query: 30  VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPANT--------IGAA 81
           +D  + ++ TSP      R+         VW P   + V DH  P            G A
Sbjct: 29  IDRQVINEYTSPQAFSGLREAGRN-----VWRPGTALAVVDHVNPTTPKRIAAMPDAGGA 83

Query: 82  EFQRVTREFAREQGI--VNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFGAF 139
                  E  R+ GI  ++I     GI H + PE+GF+ PGMVI   DSHT TYGA GAF
Sbjct: 84  RQVSYLAENCRDFGIELLDILDKRQGIEHVIAPEQGFILPGMVIAAGDSHTTTYGALGAF 143

Query: 140 ATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGATYRS 199
             G+G +++  + A+    +   + M + V G+    + +KDVI+ +IG+IG  GAT  +
Sbjct: 144 GFGIGTSEIEHLLASQTLVYKRLKTMCVSVDGDLAPGLTSKDVIMALIGKIGASGATGYA 203

Query: 200 VEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYV----RARTGR------- 248
           +EF G T++++ V  RMTICNMAVE GA+   M P+ +   Y+    RA  G        
Sbjct: 204 IEFRGSTLDALSVEARMTICNMAVEAGARGAFMAPDEKVFAYLKGKPRAPQGELWDQALA 263

Query: 249 EFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPV-------------------- 288
            +R+  SD  + + ++   D + LEP V      D   P+                    
Sbjct: 264 GWRLLHSDVGAVFDQEVQLDATTLEPMVTWGTSPDQAAPIGARVPDPQDVSDLILRQDMR 323

Query: 289 -----------HRVEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASR 337
                       R+    I  AF+GSCTN R EDL+ AA V+  + V E VR ++ P S 
Sbjct: 324 RALNYMGLEAGMRLSDIVISHAFIGSCTNARIEDLRDAASVVRGKHVAEHVRAMIVPGST 383

Query: 338 EIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPA 397
           E+  +A  +G+   FI AG      GC  CL  +  VLAPG+   ++TNRNF GR G  A
Sbjct: 384 EVRDQAEAEGLAAIFIDAGFEWRQSGCSMCLAMNDDVLAPGDRCASSTNRNFEGRQGAGA 443

Query: 398 SSVYLANPAVVAESAIEG 415
            + +L +PA+VA +AI G
Sbjct: 444 RT-HLMSPAMVAAAAITG 460


Lambda     K      H
   0.320    0.137    0.408 

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: 525
Number of extensions: 22
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 428
Length of database: 472
Length adjustment: 33
Effective length of query: 395
Effective length of database: 439
Effective search space:   173405
Effective search space used:   173405
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 Apr 09 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