GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_28230 AO353_28230
           succinate-semialdehyde dehydrogenase
          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 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, 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