GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Pseudomonas simiae WCS417

Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate GFF3634 PS417_18600 isopropylmalate isomerase

Query= BRENDA::Q58409
         (420 letters)



>FitnessBrowser__WCS417:GFF3634
          Length = 472

 Score =  219 bits (557), Expect = 2e-61
 Identities = 150/441 (34%), Positives = 226/441 (51%), Gaps = 54/441 (12%)

Query: 24  VEVDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFDHNVPPNTVK-------AAEMQK 76
           + +D  + H+ T+P A++ L+      W  D I+   DHNVP    +       A ++ +
Sbjct: 26  IYIDRHIIHEVTSPQAFEGLRLAGRKPWRVDSIIATPDHNVPTTPERKGGIDAIADQVSR 85

Query: 77  LALE----FVKRFGIKNFHKGG--EGICHQILAEN-YVLPNMFVAGGDSHTCTHGAFGAF 129
           L ++    +   +GI  F      +GI H I  E    LP M V  GDSHT THGAFGA 
Sbjct: 86  LQVQTLDDYCDEYGITEFKMNDVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFGAL 145

Query: 130 ATGFGATDMAYIYATGETWIKVPKTIRVDIVGKNE-NVSAKDIVLRVCKEIGRRGATYMA 188
           A G G +++ +++AT     K  K + V + G     V+AKDIVL V  +IG  G    A
Sbjct: 146 AHGIGTSEVEHVFATQCLVAKKMKNMLVKVEGTLPFGVTAKDIVLAVIGKIGTAGGNGHA 205

Query: 189 IEYGGEVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEITYDYLK----KERGLSDEDIAK 244
           IE+ G  ++++ ++GR+T+CNM+IE G + G++ ADE T +Y+K      +G +D D A 
Sbjct: 206 IEFAGSAIRDLSIEGRMTICNMSIEAGARVGMVAADEKTVEYVKGRPFAPQG-ADWD-AA 263

Query: 245 LKKERITVNRDEANYYKEIEIDITDMEEQVAVPHHPDNVKPISD---------------- 288
           ++  +  V+  +A +   +E+D   ++ QV+    P+ V  +                  
Sbjct: 264 VEAWKDLVSDADAVFDTVVELDAAQIKPQVSWGTSPEMVLAVDQNVPDPAKETDLVKRGS 323

Query: 289 ---------------VEGTEINQVFIGSCTNGRLSDLREAAKYLKGREVHKDVK-LIVIP 332
                          +   ++++VFIGSCTN R+ DLR AA   KGR+V   +K  IV+P
Sbjct: 324 IERALKYMGLQANQAITDIQLDRVFIGSCTNSRIEDLRAAAVIAKGRKVASTIKQAIVVP 383

Query: 333 ASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAEGEICLSTTNRNFKGRMG 392
            S  V  QA  EG+  IF++AG     PGC  CL  +   L  GE C ST+NRNF+GR G
Sbjct: 384 GSGLVKAQAEAEGLDKIFLEAGFEWREPGCSMCLAMNPDRLESGEHCASTSNRNFEGRQG 443

Query: 393 HINSYIYLASPKIAAISAVKG 413
                 +L SP +AA +AV G
Sbjct: 444 -AGGRTHLVSPAMAAAAAVNG 463


Lambda     K      H
   0.318    0.136    0.399 

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: 494
Number of extensions: 17
Number of successful extensions: 5
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: 420
Length of database: 472
Length adjustment: 32
Effective length of query: 388
Effective length of database: 440
Effective search space:   170720
Effective search space used:   170720
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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