GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas fluorescens GW456-L13

Align [amino group carrier protein]-C-terminal-L-glutamyl-γ-L-lysine aminotransferase (EC 2.6.1.118; EC 2.6.1.124) (characterized)
to candidate PfGW456L13_2301 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)

Query= metacyc::MONOMER-18314
         (387 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2301
          Length = 466

 Score =  207 bits (526), Expect = 6e-58
 Identities = 130/414 (31%), Positives = 217/414 (52%), Gaps = 49/414 (11%)

Query: 12  LTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQL-ENISILSTSFSTP 70
           L + + +  YV D+EGR ++D   G G   LGH +P+++E ++  L + + + +   +TP
Sbjct: 47  LALKRAKGIYVEDVEGRTFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTP 106

Query: 71  IKDEMLQALDKVKPDKMDNAMLLN----SGTEAVEAALKTARKITGRKKIIAFKNAFHGR 126
           +KD  +Q L  + P  +     +     +GT+AVEAALK  R  TGR  +I+F+  +HG 
Sbjct: 107 VKDRFVQDLFGLLPPALAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVISFQGGYHGM 166

Query: 127 TAGSLSVTWNKKYREPFEPLVGP-VEFLTFN-----------------NIEDLSKIDNET 168
           + G+LS+  +   ++P   L+G  V+F+ +                  N+  L  + N+ 
Sbjct: 167 SQGALSLMGSLGPKKPLGALLGSGVQFMPYPYDYRCPFGLGGAQGVKANLSYLENLLNDP 226

Query: 169 -------AAVIVEPIQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWA 221
                  AAVIVE +QGE GVIPA++++++ ++  TE  G  LI DEIQ+GF RTGK++A
Sbjct: 227 EAGVQLPAAVIVEVVQGEGGVIPADLDWLRGVRRITEQAGVALIVDEIQSGFARTGKMFA 286

Query: 222 YKHYNIVPDILTAGKAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACK 281
           ++H  I+PD++   KAIGG  P++VV   D +   L  G H  T+ GN MAMAA  A  +
Sbjct: 287 FEHAGIIPDVVVMSKAIGGSLPLAVVVYRDWLDTWL-PGAHAGTFRGNQMAMAAGCAVMR 345

Query: 282 VIEKENVVEQANQKGQQFSNILVKNLADLKVVREVRGKGLMIGIDIRFQPGQ-------- 333
            + +  V E A   G++ +  L     D   + ++RG+GLM+G+++    G         
Sbjct: 346 YLVEHKVCEHAAAMGERLAEHLRILQRDFPQLGDIRGRGLMLGVELVDPTGALDAQGHPP 405

Query: 334 --------VLKYLQEKGILAVKAG--STVIRFLPSYLITYENMEEASNVLREGL 377
                   V +   ++G++    G    V+RFLP  +IT   ++  + +    L
Sbjct: 406 AFARLAPLVQRECLKRGLILELGGRHGAVVRFLPPLVITAAQIDRVAEIFGRAL 459


Lambda     K      H
   0.317    0.136    0.385 

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: 396
Number of extensions: 26
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: 387
Length of database: 466
Length adjustment: 32
Effective length of query: 355
Effective length of database: 434
Effective search space:   154070
Effective search space used:   154070
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 (21.6 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