GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Sinorhizobium meliloti 1021

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate SM_b20259 SM_b20259 dihydrodipicolinate synthase

Query= BRENDA::A9CGZ4
         (321 letters)



>FitnessBrowser__Smeli:SM_b20259
          Length = 320

 Score =  566 bits (1458), Expect = e-166
 Identities = 283/320 (88%), Positives = 298/320 (93%)

Query: 1   MTASIFSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQR 60
           M A IFSGVIPALMTP R+DRTPDFDALVRKGK LIADGMSAVVYCGSMGDWPLLTD QR
Sbjct: 1   MKAKIFSGVIPALMTPGREDRTPDFDALVRKGKALIADGMSAVVYCGSMGDWPLLTDAQR 60

Query: 61  MEGVERLVKAGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSVIAAQKAH 120
           MEGVERLVKAG+PVIVGTGAVNTA A AHA HAQKVGA+GLMVIPRVLSRG  I AQKAH
Sbjct: 61  MEGVERLVKAGVPVIVGTGAVNTALAAAHAAHAQKVGAQGLMVIPRVLSRGPSIVAQKAH 120

Query: 121 FKAILSAAPEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 180
           FKAIL+AAP++P+VIYNSPYYGFATRADLFFALRAEH NLVGFKEFGG ADMRYAAE+IT
Sbjct: 121 FKAILAAAPDLPSVIYNSPYYGFATRADLFFALRAEHPNLVGFKEFGGNADMRYAAEHIT 180

Query: 181 SRDDEVTLMIGVDTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQAAAKGDADARAR 240
           SRDD V+LMIGVDTAV HGFVNCGATGAITGIGNVLPKEVIHLC LS+AAA GD DAR R
Sbjct: 181 SRDDGVSLMIGVDTAVFHGFVNCGATGAITGIGNVLPKEVIHLCNLSRAAAAGDVDARQR 240

Query: 241 ALELEQALAVLSSFDEGPDLVLYFKYMMVLKGDKEYTLHFNETDALTDSQRGYVEAQFKL 300
           A ELEQALAVLSSFDEGPDLVLYFK+MMVLKGDKEYTLHFNETDALT+SQRGYVEAQFKL
Sbjct: 241 AQELEQALAVLSSFDEGPDLVLYFKHMMVLKGDKEYTLHFNETDALTESQRGYVEAQFKL 300

Query: 301 FNSWYADWSKLPGAVQTCKA 320
           FN+WYA+WSKLPGAV+  KA
Sbjct: 301 FNTWYAEWSKLPGAVEKYKA 320


Lambda     K      H
   0.320    0.135    0.398 

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: 451
Number of extensions: 10
Number of successful extensions: 1
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: 321
Length of database: 320
Length adjustment: 28
Effective length of query: 293
Effective length of database: 292
Effective search space:    85556
Effective search space used:    85556
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: 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