GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Paraburkholderia bryophila 376MFSha3.1

Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate H281DRAFT_02585 H281DRAFT_02585 FAD/FMN-containing dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_02585
          Length = 461

 Score =  166 bits (421), Expect = 1e-45
 Identities = 139/471 (29%), Positives = 225/471 (47%), Gaps = 40/471 (8%)

Query: 20  ALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVVLPERIEQVETLLKLCHQRG 79
           ALLAEL A +  L     S  L+ +   GL      P  ++ P   E V   L++CH   
Sbjct: 9   ALLAELGADVVQLPAEFGSRKLQDWS--GLPG--AVPTALIRPRSTEDVARALRVCHAFS 64

Query: 80  VPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGRFARVQPGVRNLAISQAAAP 139
            PVV +G  TGL GGA  L   + L + R N+I+EVD       V+ GV    + +AA  
Sbjct: 65  QPVVTQGGLTGLVGGANALGGEVALSLERMNRIVEVDRTSATMTVEAGVPLQVVQEAALD 124

Query: 140 YELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKVDILTVEGERMTLGSDAL 199
              Y+  D  ++ +C+IGGN+A NAGG   +KYG+    +L ++ +   GE +T G   +
Sbjct: 125 AGFYFPLDLGARGSCTIGGNLATNAGGNRVIKYGMMRDQVLGIEAVLANGE-VTSGMHKM 183

Query: 200 --DSPGFDLLALFTGSEGMLGIVTEVTVKLLPKP---QVAKVLLAAFDSVEK-------- 246
             ++ G+DL  L  GSEG L ++T   ++L P+P     A   L  +D+V K        
Sbjct: 184 IKNNSGYDLRHLLIGSEGTLAVITRAVLRLRPRPTAVATAWCALPDYDAVTKLLACSQAQ 243

Query: 247 --AGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEADVHD 304
             AG +  +++ AG       ++ NL +RA  D  +  Y       +L E  G + D H 
Sbjct: 244 LSAGVSAFEVMWAGYYDA---VLANLPLRAPLDKHYPYY-------VLLESVGSDPDRHA 293

Query: 305 DC--ARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRE 362
           +   A + ++L+    ++  LA+ EA+   FW  R +A     +  P +   D +    +
Sbjct: 294 EAFEAFLGDMLEAGVVSDAALAQSEADAQAFWTIR-DAPGEYPKFIPHHSAYDVSFSISD 352

Query: 363 LPGVLKGISD-LSEQFGLRVANVF-HAGDGNMHPLILFDANQPGELERAED-LGGKILEL 419
           +  V       L E++   +  ++ H GDGN+H ++    + PG   R  D +   I ++
Sbjct: 353 VGQVAAHCEQRLQERWPDALVMIYGHLGDGNLHIVV----DIPGSEGRLHDEIDRVIYDV 408

Query: 420 CVKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGK 470
             +  GS++ EHG+G +K   +    +  E+T    +K A DP  +LNPGK
Sbjct: 409 TREFHGSVSAEHGIGVKKKAYLGHTRSDAEITAMRLIKTALDPRSILNPGK 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: 531
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: 461
Length adjustment: 34
Effective length of query: 465
Effective length of database: 427
Effective search space:   198555
Effective search space used:   198555
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 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