GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS05725
          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:

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