GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Synechococcus elongatus PCC 7942

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate Synpcc7942_0645 Synpcc7942_0645 glutamate-1-semialdehyde aminotransferase

Query= SwissProt::Q8ZPV2
         (408 letters)



>FitnessBrowser__SynE:Synpcc7942_0645
          Length = 453

 Score =  140 bits (354), Expect = 6e-38
 Identities = 110/313 (35%), Positives = 147/313 (46%), Gaps = 27/313 (8%)

Query: 22  PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNE 81
           P +  R + +  WD  G  YID+ G       GHAHP + EAL     +    G     E
Sbjct: 61  PIVFDRVKDAYAWDVDGNRYIDYVGTWGPAICGHAHPEVIEALKVAMEKGTSFGAPCALE 120

Query: 82  PALRLAKKLIDATFA-ERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHG 140
             L  A+ +IDA  + E V F NSG EA  A L+L R Y     G  K  I+ F+  +HG
Sbjct: 121 NVL--AEMVIDAVPSIEMVRFVNSGTEACMAVLRLMRAYT----GRDK--IIKFEGCYHG 172

Query: 141 RT-LFTVSAG-GQPTYSQDFAPLPP-----DIRHAAYNDLNSASALIDDNT---CAVIVE 190
              +F V AG G  T     +P  P     +   A YNDL +  AL  +N      VI+E
Sbjct: 173 HADMFLVKAGSGVATLGLPDSPGVPKSTTANTLTAPYNDLEAVKALFAENPGEIAGVILE 232

Query: 191 PVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPDILTT 250
           P+ G  G I     FL+GLRE+   H ALL+FDEV TG  R         +GVTPD+ T 
Sbjct: 233 PIVGNSGFIVPDAGFLEGLREITLEHDALLVFDEVMTGF-RIAYGGVQEKFGVTPDLTTL 291

Query: 251 AKALGGGFPIGAMLTTQDYASVMTPG---THGTTYGGNPLATAVAGKVLDIINTPEMQNG 307
            K +GGG P+GA    ++   ++ P        T  GNPLA     K L+++  P    G
Sbjct: 292 GKIIGGGLPVGAYGGKREIMQLVAPAGPMYQAGTLSGNPLAMTAGIKTLELLRQP----G 347

Query: 308 VRQRHDAFIERLN 320
             +  D   +RL+
Sbjct: 348 TYEYLDQITKRLS 360


Lambda     K      H
   0.320    0.137    0.413 

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: 438
Number of extensions: 21
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: 408
Length of database: 453
Length adjustment: 32
Effective length of query: 376
Effective length of database: 421
Effective search space:   158296
Effective search space used:   158296
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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