GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Pseudomonas putida KT2440

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate PP_3463 PP_3463 phenylacetaldehyde dehydrogenase

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



>FitnessBrowser__Putida:PP_3463
          Length = 497

 Score =  389 bits (1000), Expect = e-112
 Identities = 217/481 (45%), Positives = 290/481 (60%), Gaps = 13/481 (2%)

Query: 24  INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83
           I  ++ DA SG T    +P  G  L +V + +  D +RAV  AR  F+   WS++ P +R
Sbjct: 23  IGADWQDAASGRTLSFRNPATGEVLGEVPAAEAEDVDRAVRAARQAFDDSPWSRMRPRER 82

Query: 84  KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVA 143
           +  L R ADL+ ++  +LA LE L+ GK    +  +D+  A   + + A    K+     
Sbjct: 83  QNLLWRLADLMERDARQLAELECLNNGKSAAVAQMMDVQLAIDFLRYMAGWATKIEGSTV 142

Query: 144 PT-----PHDQL-GLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSP 197
                  P+DQ  G V RE VGVVGAIV WNFPLL+ACWKLGPALATG +VVLKP++++P
Sbjct: 143 EASMPLMPNDQFHGFVRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADETP 202

Query: 198 LTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAG 257
           L+ +++A+L  EAG PAGV NV+ G G   G AL+ H  VD L FTGST++ K L+  A 
Sbjct: 203 LSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGK-LIGKAA 261

Query: 258 ESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317
             NM R+ LE GGKSP IV  DA +LQ AA  AA+AI FNQG+VC AGSRL V R   D 
Sbjct: 262 MDNMTRVTLELGGKSPTIVMPDA-NLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKHFDN 320

Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377
            +  +       K GN LDP   +G L+  +Q + V  YIE G + GA +  GG    E 
Sbjct: 321 VVADIAGIANAMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATIACGG----EG 376

Query: 378 TG-GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTS 436
            G G +V+PT+   V    R+ QEEIFGPVL  + FD  +E + +AND PYGL A IW++
Sbjct: 377 FGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDIDEVIGMANDNPYGLGASIWSN 436

Query: 437 DISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIK 496
           D++  H+    +++GSVWVN +   D   PFGG+K SG GR+    A+E YTELK+  IK
Sbjct: 437 DLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGSAAIEHYTELKSVLIK 496

Query: 497 L 497
           L
Sbjct: 497 L 497


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: 623
Number of extensions: 30
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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: 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:

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