GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Caulobacter crescentus NA1000

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate CCNA_03663 CCNA_03663 NADP-dependent malic enzyme

Query= BRENDA::O52593
         (332 letters)



>FitnessBrowser__Caulo:CCNA_03663
          Length = 766

 Score =  137 bits (346), Expect = 7e-37
 Identities = 99/327 (30%), Positives = 158/327 (48%), Gaps = 14/327 (4%)

Query: 3   FLEQIIERAKSDVKTIVLPESTDLRVIKAASMIMKKGIAKVVLIGNE----KEIKSLAGD 58
           FL++I     ++ K IV  E  D  VI+AA      G  K +L G E    + +K +  D
Sbjct: 439 FLQKISGSVLANPKRIVFAEGEDPSVIRAAYAYQSGGFGKAILCGRENLVHENMKLVGLD 498

Query: 59  IDLEGVMIEDSLNSEKLEDYANTLYELRKSKGMTIEAARETI-KDPLYYGVMMVKKGEAD 117
            D  G+ I ++  S++  DY + LY   + +G      +  I +D   +   MV  GEAD
Sbjct: 499 PDTAGLEIINARLSDRNPDYVDALYARLQRQGYLKRDVQRLINQDRNSFAASMVTLGEAD 558

Query: 118 GMVAGAVNSTANTLRPALQILKTAPGTKLVSSFFVMVVPNCEYGHNGTFVYADCGLVENP 177
           GMV G   S    L   L+++  APG +++    V+           T   AD  + E P
Sbjct: 559 GMVTGVTRSFDQALEEVLRVVDPAPGGRIMGMSVVLA-------KGRTIFVADTNVTELP 611

Query: 178 DADQLSEIAISASKSFEMLVGAKPQVAMLSYSSYGSAKSELTEKVIKATQLAKEKAPHLA 237
           +A++L EIA  A+++   L G KP+VA +SYS++G+     +EKV +A  +  E      
Sbjct: 612 EAEELVEIACEAARAVRRL-GFKPRVAFMSYSTFGNPMGLRSEKVREAVAMLDEMEVDFE 670

Query: 238 IDGELQVDAAIVPEVAKSKAKGSSVAGKANVLIFPDLDAGNIAYKLTQRLAKAEAYGPIT 297
            +GE+  + A+ PE  ++      +   AN+LI P + A +I+ KL Q L  A   GP+ 
Sbjct: 671 YEGEMPPELALDPE-KRANYPFMRLTDSANILIMPAIHAASISTKLVQSLGGATVIGPVL 729

Query: 298 QGLARPVNDLSRGCSAEDIVGVAAITA 324
            GL++ V       S   I+ +A + A
Sbjct: 730 LGLSKSVQIAPLSASVSKILNMAMMAA 756


Lambda     K      H
   0.313    0.129    0.346 

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: 469
Number of extensions: 19
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: 332
Length of database: 766
Length adjustment: 34
Effective length of query: 298
Effective length of database: 732
Effective search space:   218136
Effective search space used:   218136
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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