GapMind for catabolism of small carbon sources

 

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

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 202865 SO3774 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, putative (NCBI ptt file)

Query= metacyc::MONOMER-11560
         (497 letters)



>lcl|FitnessBrowser__MR1:202865 SO3774 proline
            dehydrogenase/delta-1-pyrroline-5-carboxylate
            dehydrogenase, putative (NCBI ptt file)
          Length = 1059

 Score =  183 bits (465), Expect = 2e-50
 Identities = 145/462 (31%), Positives = 231/462 (50%), Gaps = 19/462 (4%)

Query: 24   INGEYTDAVSGETFECLSPVDG-RFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
            +NG+    ++GE    +SP D  + + +VA  D A   +AV +A A F S  W++     
Sbjct: 569  VNGQ---PLTGEHKTIVSPFDTTQTVGQVAFADKAAIEQAVSSAHAAFGS--WTRTPVEV 623

Query: 83   RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYD-- 140
            R + L + ADLL +N EEL  L T + GK I D    ++  A     + A    K+    
Sbjct: 624  RASALQKLADLLEENREELIALCTREAGKSIQDGID-EVREAVDFCRYYAVQAKKLMSKP 682

Query: 141  EVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200
            E+ P P  +L  +  +  GV   I PWNFPL +   ++  ALA GN+VV KP+E++ +  
Sbjct: 683  ELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSIIG 742

Query: 201  IRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQL--MVYAGE 258
             R  QLA +AGIP  VL  LPG G TVG AL     +  + FTGST  AK +   +   E
Sbjct: 743  YRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLANRE 802

Query: 259  SNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318
              +  +  E GG++  +V + +   Q   +  +S+   + G+ C+A   L ++  I D+ 
Sbjct: 803  GAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFT-SAGQRCSALRVLFLQEDIADRV 861

Query: 319  LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEET 378
            + ++  A+     GNP   +T VG ++D      + ++I+   K   KL+          
Sbjct: 862  IDVLQGAMDELVIGNPSSIKTDVGPVIDATAKANLDAHID-HIKQVGKLIKQMSLPAGTE 920

Query: 379  GGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAI--ANDTPYGLAAGIWTS 436
             G +V PT  +   +++++ ++E FGP+L VI +  +E A  I   N T +GL  GI + 
Sbjct: 921  NGHFVAPTAVE--IDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLGIHSR 978

Query: 437  DISKAHKTARAVRAGSVWVNQYDGGDMTA--PFGGFKQSGNG 476
            +   A + A  V  G+V++N+   G +    PFGG   SG G
Sbjct: 979  NEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG 1020


Lambda     K      H
   0.316    0.132    0.390 

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: 1075
Number of extensions: 60
Number of successful extensions: 4
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: 497
Length of database: 1059
Length adjustment: 40
Effective length of query: 457
Effective length of database: 1019
Effective search space:   465683
Effective search space used:   465683
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 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