GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Burkholderia phytofirmans PsJN

Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate BPHYT_RS03510 BPHYT_RS03510 FAD-binding protein

Query= reanno::Cup4G11:RR42_RS17300
         (497 letters)



>FitnessBrowser__BFirm:BPHYT_RS03510
          Length = 497

 Score =  779 bits (2011), Expect = 0.0
 Identities = 382/497 (76%), Positives = 430/497 (86%)

Query: 1   MNAPHEVSLVADDARRSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALP 60
           MNAP E++      R+  ++  L  +LP   LL++ EDTV YECDGLAAYR++P+AVALP
Sbjct: 1   MNAPAELTAEVLAQRQREVVQALMAVLPTHCLLFREEDTVAYECDGLAAYRRLPLAVALP 60

Query: 61  DNEDQVCAILRLCHSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTA 120
           + E QV  I+++CH L VP+VPRGAGT LSGGAMPI  G+V+SLA+F++IV VD  +RTA
Sbjct: 61  ETESQVQRIVQICHRLDVPIVPRGAGTGLSGGAMPIRHGVVVSLARFRKIVEVDSYARTA 120

Query: 121 VVQPGVRNLAISEAAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRV 180
            VQPGVRNL+ISEAAA Y LYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRV
Sbjct: 121 TVQPGVRNLSISEAAAPYGLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRV 180

Query: 181 RAVTMEGDVVEFGSEAPDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFD 240
           RAVTMEG++VEFGS APDAPGLDLLA +IGSEGM A+VTEV+VKLIPKPQ AQVIMASFD
Sbjct: 181 RAVTMEGEIVEFGSLAPDAPGLDLLAVLIGSEGMFAIVTEVTVKLIPKPQTAQVIMASFD 240

Query: 241 DVAKGGNAVADVIGAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEV 300
           DV KGG+AVA +I AGIIPAGLEMMDKPAT AVEEFV AGYDLDAAAILLCESDGTPEEV
Sbjct: 241 DVVKGGDAVAGIIAAGIIPAGLEMMDKPATRAVEEFVHAGYDLDAAAILLCESDGTPEEV 300

Query: 301 AEEVERMSEVLRASGASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKH 360
           A+E+ RM+ VLR  GA+RIQ+S+SE ERLRFWSGRKNAFPAAGRISPDYYCMDGT+PR+ 
Sbjct: 301 ADEIVRMTAVLREQGATRIQISRSESERLRFWSGRKNAFPAAGRISPDYYCMDGTVPRRS 360

Query: 361 IGTLLKRIEEMERKYGLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESCVE 420
           IG LL RIE ME+ Y LRC+NVFHAGDGNMHPLILF+G D DEWHRAE FGSDILE+CVE
Sbjct: 361 IGPLLARIEAMEKTYNLRCINVFHAGDGNMHPLILFNGNDLDEWHRAEAFGSDILEACVE 420

Query: 421 LGGTVTGEHGVGVEKLNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKAIPTLARCAEYG 480
           LGGTVTGEHGVG+EK+NSMCVQFS +ERD F  VK AFD   LLNPDK IPT ARCAEYG
Sbjct: 421 LGGTVTGEHGVGIEKINSMCVQFSPEERDTFHAVKRAFDAPGLLNPDKGIPTRARCAEYG 480

Query: 481 RMHVKRGLLPHPDLPRF 497
           +MHV+ GLLPHP+LPRF
Sbjct: 481 KMHVRGGLLPHPELPRF 497


Lambda     K      H
   0.319    0.136    0.402 

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: 780
Number of extensions: 20
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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