GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Cupriavidus basilensis 4G11

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate RR42_RS33075 RR42_RS33075 dihydrodipicolinate synthetase

Query= BRENDA::A9CL97
         (313 letters)



>FitnessBrowser__Cup4G11:RR42_RS33075
          Length = 313

 Score =  174 bits (441), Expect = 2e-48
 Identities = 106/306 (34%), Positives = 158/306 (51%), Gaps = 2/306 (0%)

Query: 1   MDLRGLSPAPVTAFTRDGEVDYAANAKIARWLASMEGVKSLVILGHAGEGTFLTEDERLE 60
           ++  G+ PA    F  D  ++     + ARWL    GV +L+  GH GE   LT  ER +
Sbjct: 4   INFHGIIPAIAVPFNADYSINEPELRRFARWLGGQAGVTALMTNGHTGEVFSLTPRERAQ 63

Query: 61  LIRVYVDAVGGSLPIIAGITGEGTRVAAAEAKKCKAAGATGALVYPNHGWLRFGFQRGAP 120
           + R+  DA  G  P+I+ +  EG   A  +A   K AGA G  + P H WLRFGF+    
Sbjct: 64  VTRITADATQGICPVISSVVCEGINDAVEQAGWAKEAGAAGLDIMPPHHWLRFGFKPEHC 123

Query: 121 QDRYKAIWEESGLQEILFQYPDVTKASYDLDTQLAIATQPGVVATKNGVRNMKRWYVEIP 180
            D + AI + SGL  ++  YP  T+ SY  +    +A  P V A K G R M ++  +I 
Sbjct: 124 LDYFNAIGKASGLPLVVHIYPAWTRGSYSSELLAELAKLPYVKAFKMGEREMNKYARDIK 183

Query: 181 ELKNANPNLQVLSCHDEWLLPTMFD-VDGLLVGYGNIAPELLIDLIKAGKAQDYPQARKI 239
           E++ A+P   +++CHDE+LL +M   +DG LVG+ ++ P L+ DL+KA KA D  +A ++
Sbjct: 184 EIRAADPTKVLMTCHDEYLLSSMVQGIDGALVGFASLIPGLINDLLKAVKAGDLHEAMRV 243

Query: 240 FEQLLPVTRAVYHRGSHM-EGTVALKLGLVHRGVLDHATIREPLKNLGEKAEQEIFAAFD 298
              + P+  AVY  G    E    +K  +   G+L   T+R P           I AA +
Sbjct: 244 QALINPLKDAVYGAGEPTGEAHGRMKAAMALAGILRDGTVRPPTHAPSAAELAAIRAALE 303

Query: 299 AAGIGR 304
            AG+ R
Sbjct: 304 HAGVTR 309


Lambda     K      H
   0.319    0.137    0.405 

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: 244
Number of extensions: 5
Number of successful extensions: 3
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: 313
Length of database: 313
Length adjustment: 27
Effective length of query: 286
Effective length of database: 286
Effective search space:    81796
Effective search space used:    81796
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 (21.7 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