GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Pseudomonas putida KT2440

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate PP_2930 PP_2930 putative L-serine dehydratase

Query= BRENDA::P20132
         (328 letters)



>FitnessBrowser__Putida:PP_2930
          Length = 305

 Score =  289 bits (739), Expect = 7e-83
 Identities = 155/313 (49%), Positives = 204/313 (65%), Gaps = 12/313 (3%)

Query: 7   LHVKTPIRDSMALSKMAGTSVYLKMDSAQPSGSFKIRGIGHFCKRWAKQGCAHFVCSSAG 66
           LH+ TP+ +S  LS  AG +++LK+D+ QP GSFK+RG+GH C+    +G  HFV SS G
Sbjct: 3   LHIHTPLIESRPLSLAAGRNIWLKLDALQPCGSFKLRGVGHACEVHHARGARHFVSSSGG 62

Query: 67  NAGMAAAYAARQLGVPATIVVPSTTPALTIERLKNEGATVKVVGELLDEAFELAKALAKN 126
           NAG+A AYA R+LGVP T+V+P TT     + L  E A V V G    EA  LA+ L   
Sbjct: 63  NAGLAVAYAGRKLGVPVTVVIPETTTERAKQLLHLEDAKVVVQGSSWQEANALAQTLV-- 120

Query: 127 NPGWVYIPPFDDPLIWEGHASIVKELKETLWEKPGAIALSVGGGGLLCGVVQGLQEVGWG 186
            P   +I PFDDPL+W GHAS+V E+ E    KP A+ LSVGGGGLL GVV+GL+  GWG
Sbjct: 121 GPNDAFIHPFDDPLLWAGHASLVDEVAEA-GLKPDAVVLSVGGGGLLSGVVEGLKRNGWG 179

Query: 187 DVPVIAMETFGAHSFHAATTAGKLVSLPKITSVAKALGVKTVGAQALKLFQEHPIFSEVI 246
           DVPV+A+ET GA S HAA  AG  V L +I SVA +LG K V  QAL   Q+HP+ S ++
Sbjct: 180 DVPVLAVETEGAASLHAAMQAGHSVELERIASVATSLGAKRVADQALMCVQQHPVHSHLV 239

Query: 247 SDQEAVAAIEKFVDDEKILVEPACGAALAAVYSHVIQKLQLEGNLRTPLPSLVVIVCGGS 306
           SD+ A+ A E+F+ D ++LVEPACGAALA  Y         +      L +++V+VCGG+
Sbjct: 240 SDRAALEACERFLLDHRVLVEPACGAALAVAY---------DAKALGALRNVLVVVCGGA 290

Query: 307 NISLAQLRALKEQ 319
             +L Q++A  +Q
Sbjct: 291 TATLEQIQAWLQQ 303


Lambda     K      H
   0.318    0.134    0.395 

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: 262
Number of extensions: 9
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: 328
Length of database: 305
Length adjustment: 27
Effective length of query: 301
Effective length of database: 278
Effective search space:    83678
Effective search space used:    83678
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: 48 (23.1 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