GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Lacinutrix algicola AKS293

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_055437407.1 ASC41_RS13180 aldehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_001418085.1:WP_055437407.1
          Length = 500

 Score =  191 bits (486), Expect = 4e-53
 Identities = 146/464 (31%), Positives = 229/464 (49%), Gaps = 18/464 (3%)

Query: 6   HLIGGELIADT-GRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKR 64
           + IGG+ +    G+  D  +P  G+   +   + +E +  A+DAA  AFPAW  +   +R
Sbjct: 15  NFIGGKFVDPVKGQYFDNVSPVDGKVFTQAARSTQEDIDLALDAAHEAFPAWSTSSATER 74

Query: 65  AQVLFRFKQLLEANEERIVKLISEEHGKTI-EDAAGELKRGIENVEYATAAPEILKGEYS 123
           + +L +  Q++E N E +  L + ++GK I E  A ++   I++  Y        +G  S
Sbjct: 75  SNMLLKIAQVMEDNFEYLATLETIDNGKPIRESRAADIPYCIDHFRYFAGVIRADEGSIS 134

Query: 124 RNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLL 183
            +    +      +P+GVV  I P+NFP ++  W    A+A G T ++KP+E+ P+S ++
Sbjct: 135 EHDKDTVSIVLH-EPVGVVGEIIPWNFPMLMLAWKIAPALAAGCTAVVKPAEQTPTSVIM 193

Query: 184 IAELFHEAGLPKGVLNVVHG---DKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
           + EL  +  LP GVLN+V G   + GA  AL  +  +  LSF GST     +     +  
Sbjct: 194 LMELIGDI-LPAGVLNIVTGFGAEAGA--ALATSKRIAKLSFTGSTETGRKVLHNAAENI 250

Query: 241 KRVQALGGAKNHAVLMP---DADLDNAVSALMGAAYGSC--GERCMAISVAVCVGDQIAD 295
             V    G K+  V  P   D D D    A+ GA   S   GE C A S  + V + IAD
Sbjct: 251 IPVTMELGGKSPNVFFPSVADHDDDFFSKAIEGALMFSLNQGEICTAPS-RILVHEDIAD 309

Query: 296 ALVQKLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKV 355
             ++K+  ++K +K G        +G  V+    DK+  YI  G  +GAE+V  G     
Sbjct: 310 LFIEKMKVRLKAIKTGNPLDPETMIGSQVSKPQYDKILDYIKIGKDEGAEVVAGGDAGNY 369

Query: 356 AGH-ENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCI 414
            G    G+++  T+  +   +M I++EEIFGPV+ +   +S EEA+ + ND  YG G  +
Sbjct: 370 EGELSEGYYIQPTVL-KGNNKMRIFQEEIFGPVVALTTFSSTEEAIAIANDTPYGLGAGV 428

Query: 415 FTRDGEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFG 458
           ++RD          I+ G V VN     P A+  FGG K S FG
Sbjct: 429 WSRDAHELYQVPRAIQAGRVWVNQYHTYP-AHAPFGGVKESGFG 471


Lambda     K      H
   0.319    0.137    0.411 

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: 605
Number of extensions: 34
Number of successful extensions: 5
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: 498
Length of database: 500
Length adjustment: 34
Effective length of query: 464
Effective length of database: 466
Effective search space:   216224
Effective search space used:   216224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 24 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