GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Rhodopseudomonas pseudopalustris DSM 123

Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate WP_092680947.1 BMY71_RS00235 FAD-binding protein

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



>NCBI__GCF_900110435.1:WP_092680947.1
          Length = 497

 Score =  566 bits (1459), Expect = e-166
 Identities = 276/499 (55%), Positives = 362/499 (72%), Gaps = 2/499 (0%)

Query: 1   MNILYDERVDGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVV 60
           M IL  E     L + D+  ++A L+  +P   ++  + ++KPYE DGL AYR  P++VV
Sbjct: 1   MTILMPEPDQSVLARRDQ--IVAALRKIVPGEGVISSAAEMKPYESDGLMAYRQPPMVVV 58

Query: 61  LPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGR 120
           LP   +QV  +L+ CH+ G+ VV RG+GT LSGGALPL  G+LL + +F +I E+D   R
Sbjct: 59  LPGTTQQVSEVLRYCHKHGIKVVPRGSGTSLSGGALPLADGVLLGLGKFKRIREIDFDNR 118

Query: 121 FARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL 180
              V+PGV NLAISQA      YYAPDPSSQIACSIGGN+AEN+GGVHCLKYG+T +N+L
Sbjct: 119 AVVVEPGVTNLAISQAVDHAGFYYAPDPSSQIACSIGGNIAENSGGVHCLKYGMTTNNVL 178

Query: 181 KVDILTVEGERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAA 240
             +I+ + GE + +G  A +  G+DL+ + TGSEG+LG++TEVTV++L KP+ A+ L+  
Sbjct: 179 GCEIVLMTGEILRIGGKAAECAGYDLMGVITGSEGLLGVITEVTVRILRKPETARALMVG 238

Query: 241 FDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEA 300
           F  VE AGR V DII+AGIIPGG+EMMD  +I AAE F+HAGYP+D EA+L+ ELDG + 
Sbjct: 239 FTDVEAAGRCVADIISAGIIPGGMEMMDKPAIHAAEAFVHAGYPLDVEALLIIELDGPQV 298

Query: 301 DVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPR 360
           +V +   RV  +    G+T  +++  E ER+ FW+GRK AFPAVGRISPDY CMDGTIPR
Sbjct: 299 EVDELITRVETIALGCGSTTCQISTSEKERLLFWSGRKAAFPAVGRISPDYLCMDGTIPR 358

Query: 361 RELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELC 420
            +LP VL+ ++++SE +GLRVANVFHAGDGN+HPLIL+DANQPGE+++AE  G  IL LC
Sbjct: 359 AKLPQVLRRMTEMSEHYGLRVANVFHAGDGNLHPLILYDANQPGEMDKAEAFGADILRLC 418

Query: 421 VKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAE 480
           V+VGG +TGEHGVG EK + M   F+  +L     +K AFD  GLLNPGK  PTLHRCAE
Sbjct: 419 VEVGGVLTGEHGVGIEKRDLMPEMFSDIDLNQQQRLKCAFDSEGLLNPGKVFPTLHRCAE 478

Query: 481 FGRMHIHNGQLPFPELERF 499
            GRMH+H G+  FP++ RF
Sbjct: 479 LGRMHVHGGKTAFPDIPRF 497


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: 763
Number of extensions: 27
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: 497
Length adjustment: 34
Effective length of query: 465
Effective length of database: 463
Effective search space:   215295
Effective search space used:   215295
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 24 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