GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB in Shewanella oneidensis MR-1

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)

Query= metacyc::MONOMER-13349
         (490 letters)



>lcl|FitnessBrowser__MR1:203555 SO4480 aldehyde dehydrogenase (NCBI
           ptt file)
          Length = 506

 Score =  350 bits (898), Expect = e-101
 Identities = 190/492 (38%), Positives = 287/492 (58%), Gaps = 17/492 (3%)

Query: 2   KQYRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRT 59
           ++Y N+I G+WV   + + FD+ +PV+G    ++  +D + ++ A+ A HAA + AWG+T
Sbjct: 17  EKYANFIGGKWVAPVNGKYFDNRSPVNGQNFCKIPRSDAQDIELALDAAHAA-KDAWGKT 75

Query: 60  TVAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTA 119
           +V ER+ IL RIAD +++  +    AE  + GK V      D+P    +FR FA  ++  
Sbjct: 76  SVTERSNILLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQ 135

Query: 120 PLDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSE 179
                  D       ++Y   +PLGVVG I PWN PLL+  WKIAPALA GN VV KP+E
Sbjct: 136 EGSAADID----GNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAE 191

Query: 180 ETPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIM 239
           +TP +  +L E++  + +PPGV N+V+GFG + AG+ + T+  I  + FTG +  G  I+
Sbjct: 192 QTPVSILVLLELIEDL-LPPGVLNVVNGFGAE-AGQALATSKRIAKLAFTGSTEVGFHIL 249

Query: 240 RAAATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVY 293
           + AA  + P + ELGGK+  + FAD         +K ++GM+ A F + G+VC C  RV 
Sbjct: 250 KCAAESLIPSTVELGGKSPNLYFADVMDQEDEYLDKAVEGMLLA-FFNQGEVCTCPSRVL 308

Query: 294 VERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLV 353
           ++  IY+RF++  + R + +K G P D  T +G   S E  DK+LSY  + ++EGAQVL+
Sbjct: 309 IQESIYDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLL 368

Query: 354 GGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTK 413
           GG + +    +  G+++ PTI+ G     R  +EE+FGP+  V+ F  EAEA+A+ANDT+
Sbjct: 369 GGSLCQLEGEQSKGYYISPTIMKG-HNKMRIFQEEIFGPVISVTTFKDEAEALAIANDTE 427

Query: 414 YGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNF 473
           YGL A  WT ++NR  R+   ++ G  W+N +        FGG   SGIGRE     LN 
Sbjct: 428 YGLGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLNH 487

Query: 474 YSELTNVCVRID 485
           Y    N+ V  D
Sbjct: 488 YQNTKNLLVSYD 499


Lambda     K      H
   0.321    0.137    0.420 

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: 594
Number of extensions: 21
Number of successful extensions: 8
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: 490
Length of database: 506
Length adjustment: 34
Effective length of query: 456
Effective length of database: 472
Effective search space:   215232
Effective search space used:   215232
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: 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 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