GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Pseudomonas fluorescens FW300-N2E3

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate AO353_19510 AO353_19510 aldehyde dehydrogenase

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_19510 AO353_19510 aldehyde
           dehydrogenase
          Length = 496

 Score =  381 bits (979), Expect = e-110
 Identities = 215/484 (44%), Positives = 291/484 (60%), Gaps = 13/484 (2%)

Query: 21  RAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAP 80
           R  I  E+ +A  G+T    +P  G  L  V      D +RAV  AR  F+   W++  P
Sbjct: 19  RMLIGAEWVEAADGQTMPLHNPATGEVLCVVPKATPDDVDRAVLAARNAFDDSAWTRTRP 78

Query: 81  AKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYD 140
            +R+  L + ADL+ ++ E LA LE L+ GK    +  +D+  +   + + A    K+  
Sbjct: 79  RERQNLLWKLADLMERDAELLAQLECLNNGKSAAVAQVMDVQLSIDFLRYMAGWATKIEG 138

Query: 141 EVAPT-----PHDQL-GLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSE 194
                     P DQ    + RE VGVVGAIV WNFPLL+ACWKLGPALATG +VVLKP++
Sbjct: 139 SSVEVSLPLMPDDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPAD 198

Query: 195 KSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMV 254
           ++PLTA+++A+L +EAG P+GV NV+ G G + G AL  +  VD L FTGST + KQ+  
Sbjct: 199 ETPLTALKLAELVLEAGYPSGVFNVVTGTGISAGSALTHNPLVDKLTFTGSTAVGKQIGK 258

Query: 255 YAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSI 314
            A +S M R+ LE GGKSP IV ADA DL +AA  AASAI FNQG+VC AGSRL V+R  
Sbjct: 259 IAMDS-MTRVTLELGGKSPTIVMADA-DLGSAAAGAASAIFFNQGQVCCAGSRLYVQRKH 316

Query: 315 KDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRT 374
            D  +  +       K GN LDP   +G L+  +Q   V +YIE G + GA ++ GG   
Sbjct: 317 FDNVVADIAGIANAMKLGNGLDPSVDMGPLISARQQERVYNYIEMGRESGATIVCGG--- 373

Query: 375 LEETG-GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGI 433
            E+ G G +V+PT+   V     + QEEIFGPVL  I FD   +A+ +AND+PYGL A I
Sbjct: 374 -EQFGPGFFVKPTVIVDVDQKHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASI 432

Query: 434 WTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKAT 493
           W++D++  H+    +++GSVWVN +   D   PFGG+K SG GR+    A+E YTELK+ 
Sbjct: 433 WSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELKSV 492

Query: 494 WIKL 497
            IKL
Sbjct: 493 LIKL 496


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: 618
Number of extensions: 27
Number of successful extensions: 6
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: 496
Length adjustment: 34
Effective length of query: 463
Effective length of database: 462
Effective search space:   213906
Effective search space used:   213906
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 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