GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Escherichia coli BW25113

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 16751 b2661 succinate-semialdehyde dehydrogenase I, NADP-dependent (NCBI)

Query= BRENDA::P42412
         (487 letters)



>lcl|FitnessBrowser__Keio:16751 b2661 succinate-semialdehyde
           dehydrogenase I, NADP-dependent (NCBI)
          Length = 482

 Score =  256 bits (654), Expect = 1e-72
 Identities = 150/449 (33%), Positives = 239/449 (53%), Gaps = 3/449 (0%)

Query: 11  INGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRAR 70
           INGEW+++   +  DV NPA  + L  VP    ++   A   A  A   W  +    RA 
Sbjct: 15  INGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWRALTAKERAT 74

Query: 71  ILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLASI 130
           IL N+  L+ +H+++LA L+T+E GK   EA GE+      +E+ A     + GD++   
Sbjct: 75  ILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTIPGH 134

Query: 131 ATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLVE 190
             D      + PIGV   I P+NFP  +       A+A G T +LKP+ +TP     L E
Sbjct: 135 QADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSALALAE 194

Query: 191 LFEKAGLPKGVFNVVYGAHDVV-NGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQS 249
           L  +AG+P GVFNVV G+   V N +  +P ++ +SF GS  +G  + ++ ++++K+V  
Sbjct: 195 LAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQLMEQCAKDIKKVSL 254

Query: 250 LTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKVA 309
             G     IV +DA+L+  V   + + F +AG+ C+    + V++G+ D F  KLQ+ V+
Sbjct: 255 ELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDRFAEKLQQAVS 314

Query: 310 DIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPTIF 369
            + IG+GLD+GV +GP+I E    +   +I   LE+GAR+VC G+ +    G F  PTI 
Sbjct: 315 KLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAH-ERGGNFFQPTIL 373

Query: 370 DNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRENI 429
            +V     + K+E F P+  + R K+  + I  AN +EF   A  +  + + +    E +
Sbjct: 374 VDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLSRVFRVGEAL 433

Query: 430 DAGMLGINLGVPAPMAFFPFSGWKSSFFG 458
           + G++GIN G+       PF G K+S  G
Sbjct: 434 EYGIVGINTGI-ISNEVAPFGGIKASGLG 461


Lambda     K      H
   0.318    0.136    0.396 

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: 560
Number of extensions: 30
Number of successful extensions: 3
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: 487
Length of database: 482
Length adjustment: 34
Effective length of query: 453
Effective length of database: 448
Effective search space:   202944
Effective search space used:   202944
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, the preprint on GapMind for carbon sources, 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