GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pseudomonas fluorescens FW300-N2E3

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate AO353_19510 AO353_19510 aldehyde dehydrogenase

Query= metacyc::MONOMER-16244
         (495 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_19510
          Length = 496

 Score =  413 bits (1062), Expect = e-120
 Identities = 215/496 (43%), Positives = 320/496 (64%), Gaps = 11/496 (2%)

Query: 7   VPIKLPNGTTY-EQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVE 65
           +P  LP  + + ++   + I  E+V++   +T    +P+T E +  V +A  +D+D AV 
Sbjct: 3   LPYLLPAVSAFIQRAPRMLIGAEWVEAADGQTMPLHNPATGEVLCVVPKATPDDVDRAVL 62

Query: 66  AATAAFH-SSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALT 123
           AA  AF  S+W+ + P+ R  +L+KLADL++  A+ LA +E L+NGKS   ++  DV L+
Sbjct: 63  AARNAFDDSAWTRTRPRERQNLLWKLADLMERDAELLAQLECLNNGKSAAVAQVMDVQLS 122

Query: 124 AAYFRSCAGWTDKIKGSVIETG------DTHFNYTRREPIGVCGQIIPWNFPLLMASWKL 177
             + R  AGW  KI+GS +E        D   ++ RRE +GV G I+ WNFPLL+A WKL
Sbjct: 123 IDFLRYMAGWATKIEGSSVEVSLPLMPDDQFHSFIRREAVGVVGAIVAWNFPLLLACWKL 182

Query: 178 GPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIK 237
           GP L TGCT VLK A+ TPL+AL LA L+ EAG P GV NVV+G G +AG+ ++ +P + 
Sbjct: 183 GPALATGCTVVLKPADETPLTALKLAELVLEAGYPSGVFNVVTGTGISAGSALTHNPLVD 242

Query: 238 KVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTG 297
           K+ FTGSTA G+ I K A +S + +VTLELGGKSP IV  DAD+ S      + IF+N G
Sbjct: 243 KLTFTGSTAVGKQIGKIAMDS-MTRVTLELGGKSPTIVMADADLGSAAAGAASAIFFNQG 301

Query: 298 EVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDI 357
           +VCCAGSR+YVQ   +D +V++    A ++K+G+       MG   S  Q +++  YI++
Sbjct: 302 QVCCAGSRLYVQRKHFDNVVADIAGIANAMKLGNGLDPSVDMGPLISARQQERVYNYIEM 361

Query: 358 GKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIAL 417
           G++ GAT++ GGE+FG  G+F+KPT+  DV + H +V++EIFGPV+    F    + + +
Sbjct: 362 GRESGATIVCGGEQFG-PGFFVKPTVIVDVDQKHSLVQEEIFGPVLVAIPFDDEADALRM 420

Query: 418 ANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGE 477
           ANDS YGL A + + +L+    +  +I SG++WVN ++   P +PFGGY  SG+GREMG 
Sbjct: 421 ANDSPYGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGY 480

Query: 478 EALDNYTQVKAVRIGL 493
            A+++YT++K+V I L
Sbjct: 481 AAIEHYTELKSVLIKL 496


Lambda     K      H
   0.316    0.133    0.389 

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: 635
Number of extensions: 32
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: 495
Length of database: 496
Length adjustment: 34
Effective length of query: 461
Effective length of database: 462
Effective search space:   212982
Effective search space used:   212982
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