GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Dyella japonica UNC79MFTsu3.2

Align Gamma-aminobutyraldehyde dehydrogenase; ABALDH; EC 1.2.1.19; 1-pyrroline dehydrogenase; 4-aminobutanal dehydrogenase; 5-aminopentanal dehydrogenase; EC 1.2.1.- (uncharacterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase

Query= curated2:A8GHZ8
         (474 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3729 N515DRAFT_3729
           aminomuconate-semialdehyde/2-hydroxymuconate-6-
           semialdehyde dehydrogenase
          Length = 483

 Score =  341 bits (875), Expect = 3e-98
 Identities = 201/478 (42%), Positives = 276/478 (57%), Gaps = 12/478 (2%)

Query: 6   LINGQL-VTGQGALLPVYNPATGEVVVQVAEASAEQVDQAVLAADAAFEHWGQTTPKERA 64
           LI+G+L    Q   L V+ PATGEV     E+S   VD AV AA AA   W  T  ++RA
Sbjct: 9   LIDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWAATPSEQRA 68

Query: 65  EHLLKLADLIDSHAETFARLESINCGKPYHCVLNDELPGVADVFRFFAGASRCLSGLAAG 124
             L +LADLI++  + FA LES + GKP     + ++P      R+FA A    S  +  
Sbjct: 69  RLLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIVPWSSESHA 128

Query: 125 EYLAGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEQTPLTTFKL 184
             L G  +   R PLGVVA I+PWN PL +  WK+APALAAGN VV KPSE TP T   L
Sbjct: 129 MEL-GAINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPCTAALL 187

Query: 185 AELA--AGLFPPGVLNVLFGRGASVGDRLTGHNKVRMVSLTGSIATGEHIIGHTASGIKR 242
            EL+  AG FPPGVLN++ GRG  VG  L  H  V+ VS TGS  TG  I    A   K+
Sbjct: 188 GELSIEAG-FPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAAAPRFKK 246

Query: 243 THMELGGKAPVLVFDDADLQQV-VEGIRSFGFYNAGQDCTAACRIYAQKGIYPQLVKALG 301
             +ELGGK P +VF DADL    ++ I   GF N G+ C    R+  Q+ IY    +   
Sbjct: 247 LSLELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFRERYL 306

Query: 302 EAIGSLKIGPPIDASSELGPLITAQHLERVVGFVERAKALPHVQVVTGGERVNGPG---- 357
             + +L++G P +A+++LG L++ +H ++V G + +A+A    +V+ GG+ +  PG    
Sbjct: 307 AKVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARA-EGGRVLCGGDALALPGPLAG 365

Query: 358 -YYFQPTLLAGARQEDEIVQREVFGPVVTVTPFDDEAQVLAWANESDYGLASSLWTRDVG 416
            +Y  PT++ G   E    Q+E+FGPVVT+ PFDDEAQ LA AN + YGLA+SLWT D+ 
Sbjct: 366 GWYVAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLWTTDLS 425

Query: 417 RAHRLSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTAIRHVMFKH 474
           RAHR  A+L +G  W+N   +     P GG K SG G++  +  L  +T  +++  ++
Sbjct: 426 RAHRFGAQLDFGIVWINCWLLRDLRTPFGGAKQSGVGREGGVEALRFFTEPKNICIRY 483


Lambda     K      H
   0.320    0.136    0.410 

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: 519
Number of extensions: 22
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: 474
Length of database: 483
Length adjustment: 34
Effective length of query: 440
Effective length of database: 449
Effective search space:   197560
Effective search space used:   197560
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 (21.8 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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