GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Synechococcus elongatus PCC 7942

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate Synpcc7942_2160 Synpcc7942_2160 alanine-glyoxylate aminotransferase

Query= BRENDA::P74281
         (384 letters)



>FitnessBrowser__SynE:Synpcc7942_2160
          Length = 384

 Score =  178 bits (452), Expect = 2e-49
 Identities = 112/351 (31%), Positives = 186/351 (52%), Gaps = 11/351 (3%)

Query: 4   KQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLTTSG 63
           +++L+ PGP+     VL A+++ PIGH    F +++ E+   L+++ QT+N  L +  SG
Sbjct: 23  ERLLLGPGPSNAHPAVLEAISRPPIGHLDPKFLELMTEVQGLLRYIWQTDNR-LTIPVSG 81

Query: 64  TG--AMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDFK 121
           TG  AMEA+I N + PGD VLVG  G FG+R V +A  +G  V  I   WG      + +
Sbjct: 82  TGSAAMEATIANSVEPGDVVLVGVMGYFGNRLVDMAGRYGADVRTIHKPWGDVFSLAELR 141

Query: 122 TLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAID 181
             LE   +   + L + H+ETSTG    LA +    +     L+++D VTSLGA P  +D
Sbjct: 142 QALE---EHRPQILALVHAETSTGAEQPLAGVGDLCREF-DCLLLIDTVTSLGAVPTLLD 197

Query: 182 DLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQ--AYETATIPRFYLDLKKYKKSTDEDS- 238
           + G+D+  S SQKG   PPG+   ++  +A +  A     +  +YLD+    +    D  
Sbjct: 198 EWGVDLAYSCSQKGLSCPPGVSPFTMGPRAEEKLARRKGKVANWYLDMSLLNQYWGSDRV 257

Query: 239 SPFTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAP-DNAASN 297
              T P+N+ +G++ +L+++  EG++ ++ RH+ +       ++ L L    P +N    
Sbjct: 258 YHHTAPVNMNFGIREALRLIADEGIETVWKRHRDNAEYLWAGLEDLGLTCHVPVENRLPT 317

Query: 298 AITAVAPLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRD 348
             T   P GV+ + +   +  +  I M GG   L GK++RIG +G+   R+
Sbjct: 318 LTTVRIPEGVDGKAVSRQLLDEHGIEMGGGLGELAGKVWRIGLMGYNSRRE 368


Lambda     K      H
   0.317    0.134    0.386 

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: 321
Number of extensions: 15
Number of successful extensions: 6
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: 384
Length of database: 384
Length adjustment: 30
Effective length of query: 354
Effective length of database: 354
Effective search space:   125316
Effective search space used:   125316
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: 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