GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo3_N2E3:AO353_19510
          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 (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