GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcD in Azospirillum brasilense Sp245

Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate AZOBR_RS05725 AZOBR_RS05725 FAD-binding protein

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



>lcl|FitnessBrowser__azobra:AZOBR_RS05725 AZOBR_RS05725 FAD-binding
           protein
          Length = 495

 Score =  573 bits (1478), Expect = e-168
 Identities = 281/490 (57%), Positives = 362/490 (73%), Gaps = 2/490 (0%)

Query: 10  DGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVVLPERIEQVE 69
           DG + +  +  ++A L+A +P   ++    +L+ YECDGL+AYR  P++VVLP  +EQV 
Sbjct: 8   DGVIAR--RREIIAALRAIVPGEGVIADESELRAYECDGLTAYRQLPMVVVLPSTVEQVS 65

Query: 70  TLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGRFARVQPGVR 129
            +L+ C + GV VV RGAGT LSGGALPL  G+LL M +FN+IL++D A R    QPGV 
Sbjct: 66  RVLRTCKEMGVKVVPRGAGTSLSGGALPLADGVLLGMGKFNRILDIDFANRCVVTQPGVT 125

Query: 130 NLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKVDILTVEG 189
           NL IS A A    YYAPDPSSQIAC+IGGN+AEN+GGVHCLKYGLT +N+L ++++ ++G
Sbjct: 126 NLGISTAVAHEGFYYAPDPSSQIACTIGGNIAENSGGVHCLKYGLTTNNVLGLEMVLMDG 185

Query: 190 ERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAAFDSVEKAGR 249
             + LG   LD+ G+DL+ + TGSEG+LG+VTEVTV++L KP  A+ +L  F + E+ G 
Sbjct: 186 TVLRLGGKHLDAGGYDLMGVVTGSEGLLGVVTEVTVRILKKPATARAVLIGFPTSEQGGD 245

Query: 250 AVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEADVHDDCARV 309
            V  IIAAGIIPGG+EMMD  +I AAEDF+HAGYP+D EA+L+ ELDG  A+V     +V
Sbjct: 246 CVAAIIAAGIIPGGMEMMDKPAIHAAEDFVHAGYPLDVEALLIVELDGPAAEVDHLIDQV 305

Query: 310 SEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRELPGVLKG 369
           +E+ +  G    R++  E ER+ FWAGRK AFPAVGRISPDYYCMDGTIPR+ LP VL  
Sbjct: 306 AEIARSKGCCYSRVSTSEEERLSFWAGRKAAFPAVGRISPDYYCMDGTIPRKALPLVLHR 365

Query: 370 ISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELCVKVGGSITG 429
           + ++S+++ LRVANVFHAGDGN+HPLIL+DAN+PGELERAE  G  IL LCV+VGG +TG
Sbjct: 366 MQEMSDRYALRVANVFHAGDGNLHPLILYDANKPGELERAEAFGNDILRLCVEVGGVLTG 425

Query: 430 EHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAEFGRMHIHNG 489
           EHGVG EK + M  QF+  +L     +K AFDP GLLNPGK  P LHRCAE GR+HIH G
Sbjct: 426 EHGVGVEKRDLMTDQFDEVDLDQQQRIKCAFDPDGLLNPGKVFPKLHRCAELGRVHIHKG 485

Query: 490 QLPFPELERF 499
           +L FP++ RF
Sbjct: 486 ELRFPDIPRF 495


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: 802
Number of extensions: 26
Number of successful extensions: 1
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: 495
Length adjustment: 34
Effective length of query: 465
Effective length of database: 461
Effective search space:   214365
Effective search space used:   214365
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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