GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Flavobacterium glycines Gm-149

Align Lactaldehyde reductase (characterized, see rationale)
to candidate WP_066328438.1 BLR17_RS00855 iron-containing alcohol dehydrogenase

Query= uniprot:Q8A199
         (384 letters)



>NCBI__GCF_900100165.1:WP_066328438.1
          Length = 380

 Score =  198 bits (503), Expect = 2e-55
 Identities = 129/386 (33%), Positives = 193/386 (50%), Gaps = 15/386 (3%)

Query: 4   IILNETSY-FGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYEL 62
           +ILN     FG G       +    G K+ F +   +L         I+   +N +   +
Sbjct: 5   VILNPNRVVFGEGSMQRFVDDFVASGLKRMFLIGISELAN--TLVPYIEKLKENGVAVFV 62

Query: 63  YSDVKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSLEG 122
              +K  PT  +    +    A  AD +V +GGGS +D AK +   + N    D   ++G
Sbjct: 63  DESIKGEPTFDDFNEVLEKAIAFNADSVVGVGGGSVLDVAKLVAAQLKNTQSLD--EIKG 120

Query: 123 VADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYS 182
           + + K +      +PTT+GT +EV+ N + ++ +  +K+  + P  +P  A +DP L   
Sbjct: 121 IGNLKERQTYVACIPTTSGTGSEVSPNAIFVN-NLGEKVGVISPYLVPDAAYIDPVLTVL 179

Query: 183 MPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAREA 242
           +PK +TAATG+DALTH +E+Y    A    D++ L+ + +IA+ LK A D+G D  AR  
Sbjct: 180 LPKSVTAATGIDALTHCLEAYTNKFAHPFVDLYALEGVRLIAKYLKRACDDGTDIEARTQ 239

Query: 243 MSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPKYI 302
           ++      GM    V    VH++++PLG  Y  PHG++NALLLPYVMEYN E  A+ KY 
Sbjct: 240 VALGSMYGGMCLGPVNTAAVHALSYPLGVEYHIPHGLSNALLLPYVMEYNIEEDAS-KYE 298

Query: 303 HIAKAMGV---NTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAF 359
            IA+ +G    NT   T  EGVK     +K L    G+P  L    VKEE I  LA  A 
Sbjct: 299 RIAEVLGAEKKNTSRETALEGVK----IMKQLIADCGLPTSLAHAGVKEESITKLAEGAI 354

Query: 360 N-DVCTGGNPRPTSVAEIEVLYRKAF 384
                   N R  +V +   +Y+ AF
Sbjct: 355 KVQRLLKNNIREIAVEDAVAIYQSAF 380


Lambda     K      H
   0.317    0.133    0.379 

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: 371
Number of extensions: 22
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: 384
Length of database: 380
Length adjustment: 30
Effective length of query: 354
Effective length of database: 350
Effective search space:   123900
Effective search space used:   123900
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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