GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Collimonas arenae Ter10

Align Putative oxidoreductase (characterized, see rationale)
to candidate WP_061534524.1 CAter10_RS18180 FAD-binding oxidoreductase

Query= uniprot:Q92L08
         (473 letters)



>NCBI__GCF_001584165.1:WP_061534524.1
          Length = 472

 Score =  367 bits (942), Expect = e-106
 Identities = 195/464 (42%), Positives = 286/464 (61%), Gaps = 18/464 (3%)

Query: 10  LTKLLGDKGVVTRREDMEAYEAGARYDRGRAAAVLRPVTTEEVSAAVGYCVRSGIALIPQ 69
           +  LLG +G + + E  + YE GARY  G++  + RP   +E +  +  C R  I ++PQ
Sbjct: 11  IADLLGPQGCLLQPEQRQLYEKGARYGDGKSLCIARPANVDEAAELMRLCARDKIRIVPQ 70

Query: 70  SGNTGLVSGSTPDESGSEVVVSLDRLTRQFALDLDNRSVRVDAGFRLSELNRRLEEHGLF 129
             NTGLV  ++PD SG +V++S++R+     +D  +R V+  AG RLSELN+ LE+H L+
Sbjct: 71  GANTGLVGAASPDRSGLDVLLSMERIKGVIDIDPVDRVVQAYAGTRLSELNQALEKHDLY 130

Query: 130 FPIDLGADPRIGGMIATNTGGSRFLKYGDVRRNTLGLKVVLADEAGTVLDLGSDLRKNNT 189
           FPIDLGADP +GGM+A NTGG+R ++YGDVR NTLGL+ +L D  G  LDL + LRKNNT
Sbjct: 131 FPIDLGADPSLGGMLAANTGGARLIRYGDVRHNTLGLEALLIDPPGERLDLTNRLRKNNT 190

Query: 190 GVDWKQIFIGTSGAFGIVTECVLNLERLPKQTATAFLVPASGAHVLPLLKAMEERLGAYL 249
           G DWKQ FIGT GA+G++T+ VL +   P+Q+ATA + PAS      LL+ +E     +L
Sbjct: 191 GPDWKQCFIGTGGAYGVITQVVLQVHPRPQQSATALVAPASMEAAALLLRDVERNFADFL 250

Query: 250 SAFEGMSRNAIAAAFAHVPALKNPFQGGKVPDYVILAEISRTSSPREGEQPLD----AVL 305
           SAFEG+S+NA+ +   HVP +  PF+   +P Y  L E+S ++ PR  +  L+    A L
Sbjct: 251 SAFEGISQNALQSVLQHVPGIAAPFE--PLPPYAFLIELS-SARPRSADFDLEKLFGAWL 307

Query: 306 ESVLAEIWEMEEVLLADALVGPPHEIWALRHALSEGVKHLGKLIAFDLSFRRGDIMAFCD 365
           ES   +       L+ DA++  P  +W +RHA+S+ V+  GK++AFD+S  R  +  F  
Sbjct: 308 ESCFGD-------LILDAVIDKPEVLWRIRHAISDSVRQEGKVVAFDISVPRSSLGQFRQ 360

Query: 366 HMKTEMPEKFPGVTVCDFGHIGDGGVHFNLVVAKDSPLLAD--ATFEQRLREWVFAVAVE 423
                + +   G+ + DFGH GDGG+HFNL + +   L+AD        LR+ ++ +AV 
Sbjct: 361 EAAALLEQSHAGIKLFDFGHWGDGGLHFNLAIPEQ--LIADFPPLRINALRQEIYDLAVL 418

Query: 424 QYHGSFSAEHALGRRNQAFYDLYTPEKLKNMAAGLKTLTSPGKL 467
           +Y GSFSAEH +G  NQ FY+ YT      +A  ++ +  P +L
Sbjct: 419 KYKGSFSAEHGVGPFNQQFYERYTTPAQLALATRMQNVFDPERL 462


Lambda     K      H
   0.320    0.137    0.402 

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: 572
Number of extensions: 24
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: 473
Length of database: 472
Length adjustment: 33
Effective length of query: 440
Effective length of database: 439
Effective search space:   193160
Effective search space used:   193160
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 (21.8 bits)
S2: 51 (24.3 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