GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Caulobacter crescentus NA1000

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate CCNA_03309 CCNA_03309 homoserine O-acetyltransferase

Query= SwissProt::B9L9I6
         (368 letters)



>FitnessBrowser__Caulo:CCNA_03309
          Length = 358

 Score = 78.2 bits (191), Expect = 3e-19
 Identities = 63/199 (31%), Positives = 94/199 (47%), Gaps = 25/199 (12%)

Query: 12  KPLYLESGRILEPWQIIYETYGELNEKK----DNVILITHALSGSHHAAGMYEGDRKPGW 67
           K +  +SG  L   ++ Y T G  +       DN +++ H   GS       +    P +
Sbjct: 38  KDVTFKSGERLSEARMRYTTAGTPHRNAQGEIDNAVMLLHGTGGSG------KNFLSPLF 91

Query: 68  WDGLIGDGKAIDTTKYFVISTNVIGSCFGSTSPMSPIHPGSSERYRLKFPVVTIKDMVKA 127
            D L G G+ +D  K +VI  + IG   GS+ P        S+  R+ FP     DM+  
Sbjct: 92  ADELFGPGQPLDLAKTYVIMPDNIGHG-GSSKP--------SDGLRMAFPRYDYDDMIAL 142

Query: 128 Q-KILLDSLGIRHLKAIVGGSMGGMQALRFAVDFPGFCENIIPIATTYQTKPYV---IAI 183
           Q ++L++ LG++ LK I+G SMG M A  +   +PGF E + P A      P V      
Sbjct: 143 QHRLLVEGLGVKRLKLILGTSMGCMHAFVWGQTYPGFAERLAPFAC--NAVPLVGRNRMW 200

Query: 184 NKSMIEAIRADSEFKNGNY 202
            K  ++AIRAD  +K GNY
Sbjct: 201 RKMAMDAIRADPAWKEGNY 219


Lambda     K      H
   0.322    0.141    0.422 

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: 304
Number of extensions: 11
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: 368
Length of database: 358
Length adjustment: 29
Effective length of query: 339
Effective length of database: 329
Effective search space:   111531
Effective search space used:   111531
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 (21.9 bits)
S2: 49 (23.5 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