GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Caulobacter crescentus NA1000

Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate CCNA_01818 CCNA_01818 D-alanine aminotransferase

Query= curated2:O29329
         (290 letters)



>FitnessBrowser__Caulo:CCNA_01818
          Length = 287

 Score =  139 bits (351), Expect = 6e-38
 Identities = 86/274 (31%), Positives = 145/274 (52%), Gaps = 6/274 (2%)

Query: 3   YVYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLE 62
           + Y++G FV   EA V I D G+   DGV+E    ++G++   + H  RL+ S   + + 
Sbjct: 4   FAYVNGRFVRHGEAAVHIEDRGYQLADGVYEVWAVFDGKLADAEGHFARLWRSLDELRIA 63

Query: 63  IPITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLG-LDPRKCQNPSIIVITKPWGKL 121
            P+++     ++ E +R+N +R+      VTRG+       P     PS++V  +   + 
Sbjct: 64  HPMSEAALTMVLREAVRRNKVREGLCYLQVTRGVARRDHAFPNPAVLPSVVVTARSLDRA 123

Query: 122 YGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYV 181
             +  +    A  ++V+ N +     +IKS+  L N LAK  A  +G  EA F+D  G V
Sbjct: 124 ASEA-KAAQGASVISVQENRWGRC--DIKSIGLLPNALAKQAARERGAIEAWFVDDMGLV 180

Query: 182 SEGSGDNIFVVK-NGAITTPPT-INNLRGITREAVIEIINRLGIPFKETNIGLYDLYTAD 239
           +EG+  N ++V   GA+ T  T  N LRG+TR  ++++I   G+   E    + +  +A 
Sbjct: 181 TEGASSNAWIVDAEGALRTRDTNANILRGVTRYTLLDVIRESGMVINEKPFTIAEAQSAR 240

Query: 240 EVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKL 273
           E F+TG  + + PIV +DG K+GDGKPG + ++L
Sbjct: 241 EAFITGAGSLVTPIVQVDGVKLGDGKPGPVAKRL 274


Lambda     K      H
   0.319    0.142    0.409 

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: 201
Number of extensions: 9
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: 290
Length of database: 287
Length adjustment: 26
Effective length of query: 264
Effective length of database: 261
Effective search space:    68904
Effective search space used:    68904
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