GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Thermoactinomyces daqus H-18

Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate WP_033102282.1 JG50_RS0116910 FAD-binding protein

Query= reanno::psRCH2:GFF3772
         (499 letters)



>NCBI__GCF_000763315.1:WP_033102282.1
          Length = 470

 Score =  340 bits (871), Expect = 8e-98
 Identities = 169/419 (40%), Positives = 260/419 (62%), Gaps = 1/419 (0%)

Query: 56  PLLVVLPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEV 115
           P +VV P+   ++  ++KL ++  +PV  RG GT LSGG LP+  GI+L M R NK+L +
Sbjct: 41  PDVVVFPQSATEIAEIMKLANREQIPVTPRGGGTSLSGGPLPVAGGIVLAMTRMNKLLRI 100

Query: 116 DPAGRFARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLT 175
           D     A V+PG+    + + A    L+Y PDPSS    +IGGN+AEN+GG H LKYG+T
Sbjct: 101 DRDNLIAFVEPGITTAELQREAEKAGLFYPPDPSSSNVSTIGGNLAENSGGPHGLKYGVT 160

Query: 176 VHNLLKVDILTVEGERMTLGSDALDS-PGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVA 234
            H ++ ++++T +GE +  G   + +  G+DL +L  GSEG LGI+T+  ++L+PKP   
Sbjct: 161 KHYVIGLEVVTPQGEIIRTGGMTVKNVTGYDLTSLIVGSEGTLGIITKAVLRLIPKPPAR 220

Query: 235 KVLLAAFDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCE 294
           K L+A FD +  +GRA+  I+  GI+P  LEMMD  SIRA E++  +G P+DA AILL E
Sbjct: 221 KALMAIFDEIVDSGRAISGILKNGILPAKLEMMDQASIRAVENYQPSGLPLDAAAILLLE 280

Query: 295 LDGVEADVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCM 354
           +DG  A V ++  + +++ +   A EVRLA DEAER   W  RK   PA+ ++ P     
Sbjct: 281 VDGHPAAVDEEIRKAAQICRQYAAREVRLAADEAERAELWKARKLVSPAISQVKPTKISE 340

Query: 355 DGTIPRRELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGG 414
           D T+PR ++P +L+ +  + E++ L +    HAGDGN+HP I+ D+    E++R E+   
Sbjct: 341 DATVPRSKIPEMLERLRQIREKYQLHLVVFGHAGDGNLHPNIIADSRDRDEMKRVEEAVA 400

Query: 415 KILELCVKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIP 473
           +I +  V++GG+++GEHG+G  K   M  +  +  L +   +K A+DP+ +LNP K  P
Sbjct: 401 EIFKAAVELGGTLSGEHGIGTMKPAFMEMELGSAGLDMMRRIKQAWDPNNILNPFKIFP 459


Lambda     K      H
   0.320    0.140    0.412 

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: 562
Number of extensions: 19
Number of successful extensions: 2
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: 499
Length of database: 470
Length adjustment: 34
Effective length of query: 465
Effective length of database: 436
Effective search space:   202740
Effective search space used:   202740
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: 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