GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pseudomonas simiae WCS417

Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate GFF3809 PS417_19505 2,4-diaminobutyrate 4-aminotransferase

Query= curated2:Q976K0
         (387 letters)



>FitnessBrowser__WCS417:GFF3809
          Length = 464

 Score =  221 bits (563), Expect = 3e-62
 Identities = 142/404 (35%), Positives = 226/404 (55%), Gaps = 49/404 (12%)

Query: 12  LTIVKGEGQYVWDISGTKYLDLHTGIGVAFLGHRNRRVIEYLSRQMENIMTLST-SFSTP 70
           L + + +G YV D+ G +++D   G G   LGH +  VIE + + + + + L T   +TP
Sbjct: 45  LALKRAKGLYVEDVEGRRFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTP 104

Query: 71  IRDEMLKELDPLKPDKMDNIILLN----SGTEAVEAALKTARKITGRKKIIAFKNSFHGR 126
           ++D+ +++L  L P  +     +     +GT+AVEAALK  R  TGR  +++F+  +HG 
Sbjct: 105 VKDQFVQDLFGLLPPALAREAKIQFCGPTGTDAVEAALKLVRTATGRSTVLSFQGGYHGM 164

Query: 127 TAGSLSVTWNKRYREPFEPLM-SPVQFLTY--------------------NNIDELKNID 165
           + G+LS+  +   ++P   L+ + VQFL Y                    + +D L N  
Sbjct: 165 SQGALSLMGSLGPKKPLGALLGNGVQFLPYPYDYRCPFGLGGAEGVRVNLHYLDNLLNDP 224

Query: 166 EQ----TAAVIVEPIQGESGVIPANEDFMKALREQTQKVGALLVVDEVQTGFGRTGKVWA 221
           E      AAVIVE +QGE GVIPA+ D+++ LR  T++ G  L+VDE+Q+GFGRTGK++A
Sbjct: 225 EAGVLLPAAVIVEVVQGEGGVIPADLDWLRGLRRITEQAGVALIVDEIQSGFGRTGKLFA 284

Query: 222 YQHYGIIPDLLTAGKAIGGGFPVSALFLPDWIAEKLEEGDHGSTYGGNPMAMAAVTAASK 281
           ++H GIIPD++   KAIGG  P++ +   DW+   L  G H  T+ GN MAMAA +A  +
Sbjct: 285 FEHAGIIPDVVVMSKAIGGSLPLAVVVYRDWLDTWL-PGAHAGTFRGNQMAMAAGSAVMR 343

Query: 282 VLKEDNVVEQASIKGEIFKKILREKLSDLKSVREIRGKGLMIGIEI----------RFPP 331
            LK+ ++   A+  GE   + LR    D   + +IRG+GLM+G+E+            PP
Sbjct: 344 YLKDHDLAGHAAAMGERLGEHLRILQRDFPHLGDIRGRGLMLGVELVDPNGTLDVQGHPP 403

Query: 332 A---IALKVMQD--ERVLALKAG---STVIRFLAPYMITQSDME 367
               +A  V ++  +R L L+ G    +V+RFL P +IT  +++
Sbjct: 404 VHRQLAPLVQRECLKRGLILELGGRHGSVVRFLPPLVITAVEVD 447


Lambda     K      H
   0.318    0.135    0.383 

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: 422
Number of extensions: 20
Number of successful extensions: 4
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: 464
Length adjustment: 32
Effective length of query: 355
Effective length of database: 432
Effective search space:   153360
Effective search space used:   153360
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