GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Pedobacter sp. GW460-11-11-14-LB5

Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase (EC 2.6.1.11) (characterized)
to candidate CA265_RS15205 CA265_RS15205 aspartate aminotransferase family protein

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



>FitnessBrowser__Pedo557:CA265_RS15205
          Length = 378

 Score =  249 bits (637), Expect = 7e-71
 Identities = 137/374 (36%), Positives = 221/374 (59%), Gaps = 20/374 (5%)

Query: 12  LTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLE---NISILSTSFS 68
           L  V+ +  Y++D + ++++D   GIGV+ +GH +P +++ ++ Q E   ++ +      
Sbjct: 2   LEFVRAKGIYIYDAQNKKHIDLIAGIGVSNVGHCHPAVVKAIQEQAETYMHLMVYGEYVQ 61

Query: 69  TPIKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFKNAFHGRTA 128
           TP +    +AL  + P+ +     LNSGTEAVE A+K A++ TGRK  IA KNA+HG T 
Sbjct: 62  TP-QVNFAKALADILPESLSCTYFLNSGTEAVEGAMKLAKRYTGRKGFIACKNAYHGSTQ 120

Query: 129 GSLSVTWNKKYREPFEPLVGPVEFLTFNNIEDLSKIDNETAAVIVEPIQGESGVIPANIE 188
           G+ S+  +  Y   + P +  V F+  NN+ DL KI NE AAV +EPIQGE+G+  +++ 
Sbjct: 121 GAESLMESDFYSSGYGPFLPHVSFIEHNNLADLEKITNEIAAVFIEPIQGEAGIRVSDLS 180

Query: 189 FMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAGKAIGGGFPVSVVF 248
           +M+AL+ K   TG+LLIFDEIQ+GFGR+GK++A++HYN+VPD+L   K IGGG P+    
Sbjct: 181 YMQALRTKCTETGTLLIFDEIQSGFGRSGKMFAFEHYNVVPDVLLLAKGIGGGMPIGAFI 240

Query: 249 LPDHIANKLEEG---DHGSTYGGNPMAMAAVTAACKVIEKENVVEQANQKGQQFSNILVK 305
               I + L       H +T+GG+P+  AA  A  + +  +++V++  +KGQ F     K
Sbjct: 241 SSLEIMSVLSHTPILGHMTTFGGHPVCCAAGLATLRTLVDDHIVDEVEEKGQLF-----K 295

Query: 306 NLADLKVVREVRGKGLMIGIDIRFQPGQVLKYLQEKGILAVKAG------STVIRFLPSY 359
            L     ++E+RGKGLM+ ++  F+  ++ K + +  IL           S  +R  P  
Sbjct: 296 QLLQHPAIKEIRGKGLMLAVE--FENFEINKKIIDACILDGVLSDWFLHCSNSMRIAPPL 353

Query: 360 LITYENMEEASNVL 373
           +IT E + EA  ++
Sbjct: 354 IITKEEIAEACTII 367


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: 366
Number of extensions: 15
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: 378
Length adjustment: 30
Effective length of query: 357
Effective length of database: 348
Effective search space:   124236
Effective search space used:   124236
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: 50 (23.9 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