GapMind for catabolism of small carbon sources

 

Aligments for a candidate for amaB in Caulobacter crescentus NA1000

Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate CCNA_00865 CCNA_00865 alpha-ketoglutaric semialdehyde dehydrogenase xylA

Query= SwissProt::Q64057
         (539 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00865 CCNA_00865 alpha-ketoglutaric
           semialdehyde dehydrogenase xylA
          Length = 478

 Score =  233 bits (595), Expect = 9e-66
 Identities = 149/455 (32%), Positives = 230/455 (50%), Gaps = 10/455 (2%)

Query: 71  PAN-NEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGDALREKIQLLG 129
           P+N N+ +A+V      + +  +  A+KA+  WAD     R +++ K+G  +  +   +G
Sbjct: 25  PSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEVRSDLLDKVGSTIIARSADIG 84

Query: 130 RLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSERPGHALMEQWNPLGLVG 189
           RL++ E GK L EGIGE      +  Y AG +    G  L S RPG  +      +G+ G
Sbjct: 85  RLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRRHGQNLESTRPGVEIQTYRQAVGVYG 144

Query: 190 IITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKIIAKVLEDNLLPGAICS 249
           +IT +NFP+A+  W  A AL  GN  + K A  T     A   ++A ++ +   P  + +
Sbjct: 145 LITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTP----ATANVLADIMAECGAPAGVFN 200

Query: 250 LTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSLLELGGNNAIIAFEDA 309
           +  G   MG A+ + + V+ +SFTGS  VG QVA     R  +  LE+GG N +I  +DA
Sbjct: 201 MLFGRGSMGDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQARVQLEMGGKNPLIVLDDA 260

Query: 310 DLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNAYSQIRVGNPWDPNILY 369
           DL   +  AL  +    GQRCT   RL + + IHD+ V  L    + +RVG+  DPN   
Sbjct: 261 DLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLAEKVAALRVGDALDPNTQI 320

Query: 370 GPLHTKQAVSMFVQAVEEAKKEGGTVVYGGK--VMDHPGNYVEPTIVTGLVHDAPIVHKE 427
           GP  ++  +    + ++ A  EGG VV GG    +D+PG YV PT++        I ++E
Sbjct: 321 GPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNPGWYVRPTLIADTQAGMRINNEE 380

Query: 428 TFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPT 487
            F P+    + K+ EE  E  N V+ GLS+ I T  L     +   + +  G+  VN+ T
Sbjct: 381 VFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHARHF--QRYARAGMTMVNLAT 438

Query: 488 SGAEIGGAFGGEKHTG-GGRESGSDAWKQYMRRST 521
           +G +    FGG K +  G RE G  A + + +  T
Sbjct: 439 AGVDYHVPFGGTKSSSYGAREQGFAAVEFFTQTKT 473


Lambda     K      H
   0.319    0.137    0.417 

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: 663
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 539
Length of database: 478
Length adjustment: 34
Effective length of query: 505
Effective length of database: 444
Effective search space:   224220
Effective search space used:   224220
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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