GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Pseudomonas putida KT2440

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate PP_0213 PP_0213 succinate-semialdehyde dehydrogenase (NADP+)

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__Putida:PP_0213
          Length = 480

 Score =  538 bits (1386), Expect = e-157
 Identities = 267/478 (55%), Positives = 356/478 (74%), Gaps = 8/478 (1%)

Query: 44  ADLLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWK 101
           A L R  +++ G WL      T  V +PA+G  +GTV   G  E R A+ AA  A  +W+
Sbjct: 6   AQLFRQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWR 65

Query: 102 EISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARR 161
            ++ KERS+ LR+W++LMI+N+D+LA+++T E GKPL EA+GEI Y+A F+EWF+EEA+R
Sbjct: 66  ALTAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKR 125

Query: 162 VYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDT 221
           +YGD I     DKR +V+KQP+GV + ITPWNFP+AMITRK G ALAAGCT+V+KPA  T
Sbjct: 126 IYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQT 185

Query: 222 PYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILL 281
           PYSALAL +LA++AGIP GV +V+  S   A EVG  L  + LV K+SFTGST  G+ L+
Sbjct: 186 PYSALALVELAHRAGIPAGVLSVVTGS---AGEVGGELTGNSLVRKLSFTGSTEIGRQLM 242

Query: 282 HHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIH 341
              A  +K+VS+ELGG APFIVFD A++D+AV GA+ SK+RN GQTCVC+NR  VQ G++
Sbjct: 243 EECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVY 302

Query: 342 DSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRH 401
           D+F  K A A+ K L++GNG EEGTT GPLI+ KAV KV++H+ DAV+KGA V++GGK  
Sbjct: 303 DAFAEKLAAAVAK-LKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI 361

Query: 402 QSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQ 461
           +  GNFFEPT+L +V +      EETFGP+AP+ +F  E E +A++N  + GLA YFY++
Sbjct: 362 E--GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419

Query: 462 DPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVC 519
           D ++++RVAE LE GMVG+N GLIS+   PFGG+K SGLGREGSKYGI++YLE+KY+C
Sbjct: 420 DMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 477


Lambda     K      H
   0.318    0.135    0.400 

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: 624
Number of extensions: 23
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: 523
Length of database: 480
Length adjustment: 34
Effective length of query: 489
Effective length of database: 446
Effective search space:   218094
Effective search space used:   218094
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 (21.7 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