GapMind for catabolism of small carbon sources

 

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

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate AO353_28230 AO353_28230 succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_28230
          Length = 485

 Score =  493 bits (1268), Expect = e-144
 Identities = 257/480 (53%), Positives = 333/480 (69%), Gaps = 7/480 (1%)

Query: 46  LLRGDSFVGGRWL--PTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           LL   +++ G+W+     AT  V DPA+G  L  V      E R A+ AA  A+ +W+  
Sbjct: 11  LLAELAYIDGQWIGADNAATLDVIDPANGQLLARVPAMQGTETRRAIDAAEKAWPAWRAR 70

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
              ER++LL +WY  MI N D+LA I+T E GKPL EA+GEI Y A F++WF+EEARRVY
Sbjct: 71  PAAERAALLERWYQAMIDNLDDLALIMTCEQGKPLNEAKGEIRYGAGFVKWFAEEARRVY 130

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           G+ I   + D+R L LKQPVGV + ITPWNFP+AMITRK   ALAAGC ++VKP++ TP 
Sbjct: 131 GETIPAPSGDRRLLTLKQPVGVCAAITPWNFPNAMITRKCAPALAAGCPIIVKPSDLTPL 190

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           SALALA LA + GIP GV+NV+         +GE L  +P V KISFTGSTA G++L+  
Sbjct: 191 SALALAVLAERVGIPAGVFNVL---TGMPAGIGEELTGNPSVRKISFTGSTAVGRLLMRQ 247

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
           +A  +KR+S+ELGG APFIVFD A+++QAVAG M SKFRNAGQTCVC+NR LVQ GI++ 
Sbjct: 248 SAEHIKRLSLELGGNAPFIVFDDADLEQAVAGIMLSKFRNAGQTCVCANRILVQDGIYER 307

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  +  E + K L+VGNG +   T GPLIN  AV KV +H++DA+++GA ++ GG   + 
Sbjct: 308 FAQRLVEEVGK-LKVGNGLDADVTIGPLINPAAVSKVARHIDDALSQGARLLCGG-IPEG 365

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
              F +PT+L +    ML   EETFGPVAP+++F +E EA+A+ANA   GL  Y+++QD 
Sbjct: 366 DSQFVQPTVLGDAHAGMLLANEETFGPVAPLMRFTEEAEALALANATPYGLGAYYFTQDL 425

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523
            + WR  E LE GMVG+N G+IS    PFGG+KQSGLGREGSKYG+DEYLEVK    GGL
Sbjct: 426 RRSWRFGEALEFGMVGLNTGIISMEVAPFGGIKQSGLGREGSKYGLDEYLEVKAFHIGGL 485


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: 619
Number of extensions: 14
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: 485
Length adjustment: 34
Effective length of query: 489
Effective length of database: 451
Effective search space:   220539
Effective search space used:   220539
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