GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nbaE in Pseudomonas fluorescens GW456-L13

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate PfGW456L13_3517 Aldehyde dehydrogenase (EC 1.2.1.3)

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3517 Aldehyde
           dehydrogenase (EC 1.2.1.3)
          Length = 506

 Score =  332 bits (851), Expect = 2e-95
 Identities = 185/496 (37%), Positives = 280/496 (56%), Gaps = 27/496 (5%)

Query: 3   QYRNYINGEWVE--SARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60
           +Y N+I GE+V   +   F + +PV+G V+A+   +    +D A+ A HAA   AWG+T+
Sbjct: 18  RYGNFIGGEFVAPINGEYFTNTSPVNGEVIAEFPRSSAADIDKALDAAHAAA-DAWGKTS 76

Query: 61  VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120
             +R+ +L +IAD I++  +     E  D GK V      D+P  A +FR FA  ++   
Sbjct: 77  AQDRSLVLLKIADRIEQNLEVLAVTETWDNGKAVRETLNADVPLAADHFRYFAGCIRAQE 136

Query: 121 LDTFQTDLPDGARALN-----YAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVA 175
                     GA  +N     Y   +PLGVVG I PWN PLL+  WK+APALA GN +V 
Sbjct: 137 ---------GGAAEINELTTAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVL 187

Query: 176 KPSEETPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTG 235
           KP+E+TP +  + AE++  + +P GV N+V GFG + AGE + T+  I  I FTG +  G
Sbjct: 188 KPAEQTPLSIMVFAELIADL-LPAGVLNIVQGFGRE-AGEALATSKRIAKIAFTGSTPVG 245

Query: 236 SAIMRAAATHVKPVSFELGGKNAAIIFAD------CDFEKMIDGMMRAVFLHSGQVCLCA 289
           + IM  AA ++ P + ELGGK+  I F D         EK  +G++ A F + G+VC C 
Sbjct: 246 AHIMHCAAENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLA-FFNQGEVCTCP 304

Query: 290 ERVYVERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGA 349
            R  V+  IY  F+   ++++  +K G P D  T +G   S +  DK+LSY  +A+EEGA
Sbjct: 305 SRALVQESIYEPFMAEVMKKIVKIKRGNPLDTETMVGAQASEQQYDKILSYLTIAQEEGA 364

Query: 350 QVLVGGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALA 409
           ++L GG   +      +G++++PT++ G     R  +EE+FGP+  V+ F  EAEA+A+A
Sbjct: 365 ELLTGGAAERLEGDLSSGYYIQPTLLKG-HNKMRVFQEEIFGPVVGVTTFKDEAEALAIA 423

Query: 410 NDTKYGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMH 469
           ND+++GL A  WT ++NR +R+  A++ G  W N + L      FGG   SG+GRE    
Sbjct: 424 NDSEFGLGAGLWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRENHKM 483

Query: 470 SLNFYSELTNVCVRID 485
            L+ Y +  N+ V  D
Sbjct: 484 MLDHYQQTKNLLVSYD 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: 614
Number of extensions: 29
Number of successful extensions: 7
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 (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 paper from 2022 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