GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Cupriavidus basilensis 4G11

Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate RR42_RS17285 RR42_RS17285 2-hydroxy-acid oxidase

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



>FitnessBrowser__Cup4G11:RR42_RS17285
          Length = 472

 Score =  225 bits (573), Expect = 3e-63
 Identities = 141/415 (33%), Positives = 208/415 (50%), Gaps = 7/415 (1%)

Query: 59  VVLPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPA 118
           VV     E+V  + +LC++  VP++A GAG+ L G  L +  GI L ++  NK+L V P 
Sbjct: 56  VVFAHTTEEVAEVARLCNEHRVPLIAYGAGSSLEGHLLAVAGGISLDLSEMNKVLSVQPE 115

Query: 119 GRFARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHN 178
                VQPGV    ++Q      L++  DP +    S+GG  A  A G + ++YG    N
Sbjct: 116 DLNVTVQPGVTRKQLNQEIKDSGLFFPIDPGAD--ASLGGMCATRASGTNAVRYGTMREN 173

Query: 179 LLKVDILTVEGERMTLGSDAL-DSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVL 237
           +L + ++T +G  +  G+ A   S G+DL  L  GSEG LGI+TEVTV+L P+P+     
Sbjct: 174 VLALTVVTADGRIIKTGTHARKSSAGYDLTRLMIGSEGTLGIITEVTVRLYPQPEAISAA 233

Query: 238 LAAFDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDG 297
           + +F S+  A RA  + I  G+    +E +D L+IRA     H    +     L  E  G
Sbjct: 234 ICSFPSMGSAVRATIETIQLGVPVARVEFVDALAIRAINR--HDNLSMPEAPHLFFEFHG 291

Query: 298 VEADVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCM--D 355
            EA V +    V ++    G      A    +R R W  R  A+ A+ ++ P    +  D
Sbjct: 292 TEAGVKEQAETVQQIAADNGGQGFEWATRPEDRSRLWNARHTAYFAMLQLKPGCKAVTTD 351

Query: 356 GTIPRRELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGK 415
             +P   L   +           L    V H GDGN H  IL D  +P EL  AE +  +
Sbjct: 352 VCVPISRLADCVTETERDLNASSLPCPIVGHVGDGNFHVAILTDPEKPEELAEAETINRR 411

Query: 416 ILELCVKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGK 470
           I+E  + +GG+ TGEHGVG  K++ + S+   D L L  A+K A DP+ +LNPGK
Sbjct: 412 IVERALAMGGTCTGEHGVGLHKMDFLVSEHGEDALDLMRAIKNALDPNHILNPGK 466


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: 537
Number of extensions: 29
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: 499
Length of database: 472
Length adjustment: 34
Effective length of query: 465
Effective length of database: 438
Effective search space:   203670
Effective search space used:   203670
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 17 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