GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Lutibaculum baratangense AMV1

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_023431853.1 N177_RS08305 aldehyde dehydrogenase family protein

Query= reanno::Smeli:SMc00781
         (498 letters)



>NCBI__GCF_000496075.1:WP_023431853.1
          Length = 484

 Score =  247 bits (631), Expect = 6e-70
 Identities = 161/477 (33%), Positives = 248/477 (51%), Gaps = 12/477 (2%)

Query: 5   GHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAA-QPKWAATNPQ 63
           G FIDG+  A  SGR     NPATG +   V  A   D+  AV SA+AA +  W      
Sbjct: 11  GLFIDGRFSAPLSGRSFATSNPATGSLITHVGEADAVDVDRAVRSARAAFEGPWGHMRAA 70

Query: 64  RRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKG-DIVRGLEVCEFVIGIPHLQKSE 122
            R R+  +  +L+ +N++EL ++ S + GK +   +  D+   L+   +  G       +
Sbjct: 71  ERGRLLSRLAELVGENLDELVDLESLDSGKPVSAIRRQDLPAVLDTLTYYAGWADKINGQ 130

Query: 123 FTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPSVP 182
                   +  Y++R+P+G+   I P+NFP MI +W  APA+ACG   +LKP+E      
Sbjct: 131 VIPARADALT-YTVREPIGVVGAIVPWNFPLMIGVWKLAPALACGCTVVLKPAELTSLTA 189

Query: 183 IRLAELMIEAGLPAGILNVVNG-DKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMNG 241
           +RL EL +EAG PAG+LNVV G  K A  A++ HPD+  V+F GS  + R +  +AA N 
Sbjct: 190 LRLGELAMEAGFPAGVLNVVPGLGKTAGAALVDHPDVDKVTFTGSPAVGRQILRSAAGNL 249

Query: 242 KRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLIDK 301
           KR     G K+  +I PDAD++ AA A     + ++G+ C A S  V V E+  + ++++
Sbjct: 250 KRVTLELGGKSANVIFPDADVEAAAKAAAAGIFFNSGQVCSAGS-RVLVHEDVHDEVVER 308

Query: 302 LVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYEN 361
           LV     LR+G   D    MGP+V++   +R+   ++ G  +GA + V G     +  + 
Sbjct: 309 LVDRAARLRLGDPLDPATQMGPLVSETQMERVLGYVEIGRREGATVAVGGG----RVGDE 364

Query: 362 GHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGD 421
           G F+   +   V  DM + + EIFGPV+SVVR R+ EEA+ +     Y     +++ D  
Sbjct: 365 GCFVAPTVLTGVEHDMRVSQEEIFGPVVSVVRFRDEEEAVRMANGTAYSLAAGVWSSDLG 424

Query: 422 AARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTI 478
                A RI  G V VN   P  +    +GG + S FG   +HG  +I+ +T  K +
Sbjct: 425 RIHRLAKRIRAGTVWVNTFGPTDIRL-PWGGSRDSGFG--REHGEAAIENFTEPKAV 478


Lambda     K      H
   0.319    0.137    0.409 

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: 565
Number of extensions: 32
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: 484
Length adjustment: 34
Effective length of query: 464
Effective length of database: 450
Effective search space:   208800
Effective search space used:   208800
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