GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Frischella perrara PEB0191

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_052236884.1 FPB0191_RS08270 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_000807275.1:WP_052236884.1
          Length = 803

 Score =  718 bits (1853), Expect = 0.0
 Identities = 363/802 (45%), Positives = 503/802 (62%), Gaps = 26/802 (3%)

Query: 9   SVVRFLTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYA 68
           +V+  L  L  ++ G  +L GGIWL ++GGS YY++ GA M+  A L++R N  ALV+YA
Sbjct: 5   NVLSTLVGLILIVMGVVLLGGGIWLISLGGSCYYLLCGAVMIACAILVFRHNKLALVIYA 64

Query: 69  LLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGKGALGAMGVALV 128
           +LL  +  W VWEVG ++W L PR  V  + G  L+LP + + +      ++  +  +L+
Sbjct: 65  ILLCFSTIWAVWEVGLNWWQLVPRLWVWFVMGWVLLLPPIRKTMMNNRLSSIMLL-TSLI 123

Query: 129 ASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFSPLKQI 188
            +  V   S+F  P V+ G +  T  N  +A P+  +A  DW AY     G  +S L QI
Sbjct: 124 VTTVVSVASLFTSPGVIEGKIENT--NLFRANPMQ-VAAEDWIAYGGTNAGLHYSALNQI 180

Query: 189 NHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATGKQ 248
             +N+ +LQ  W+ +TGDM    DP E+T+E TP+K+ D LY CT H  + AL+  TGK 
Sbjct: 181 VPNNIHKLQEVWRIRTGDMPTADDPVELTNENTPLKVNDKLYTCTAHGWVLALEPETGKT 240

Query: 249 KWKFDPGLKTNP--TFQ---HVTCRGVSYHE-------FPAAKDASNTQPALCSRRIYLP 296
            WKFDP +  +   TF+   H+TCRG+SY++       F   K A   + + C RRIYLP
Sbjct: 241 LWKFDPAISNSGAGTFKGWAHMTCRGLSYYDSDRYLKQFAKDKIALKVKSSSCPRRIYLP 300

Query: 297 VNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVT 356
             D RL AL+A+ G+ C +FG NG++DL       TPG Y  TSP ++T   +++ G VT
Sbjct: 301 TADARLIALNADNGQLCDSFGVNGQVDLTQGIGKFTPGGYYSTSPALVTKQLVIVGGHVT 360

Query: 357 DNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKL 416
           DN ST EPSG +R FD+  G L+W +D G  D       +  +T NSPN W+    D  L
Sbjct: 361 DNESTNEPSGVVRAFDIYDGHLVWNWDSGNPDATTPLPKDKKYTRNSPNVWSITSADEAL 420

Query: 417 DIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQP 476
            +VYLP+G  TPD +GGNRTP  E+YA+ ++AL+ T+GK+VW+YQ  HHDLWDMD+P+QP
Sbjct: 421 GLVYLPLGNQTPDQYGGNRTPVVEKYAAGIVALDITSGKVVWNYQFTHHDLWDMDVPAQP 480

Query: 477 TLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPY 536
            L D+    G   P +  P K G+++VL+R+TG+ +VP  E  VPQGA KGD  S TQ  
Sbjct: 481 ILVDLKTTQG-IEPAVIQPTKQGSLYVLNRKTGQPIVPINEVSVPQGAVKGDWTSPTQAR 539

Query: 537 SELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEW 596
           S+L   P   L ++DMWGAT +DQL CR+ FK LRYEG +TPPS QG+L++PGN+G+  W
Sbjct: 540 SQLNLLPPP-LREQDMWGATPFDQLSCRIKFKSLRYEGQYTPPSLQGSLIYPGNVGVMNW 598

Query: 597 GGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGV 656
           GG+++DP R+I  A+P  + F SKLIP+     E P   A    G   G+QP  G PY V
Sbjct: 599 GGVAIDPVRKIIFASPNYMAFTSKLIPQA----EVPKNEANASEG--AGLQPNQGAPYAV 652

Query: 657 ELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSP-VPLPFKMGMPMLGG 715
            + PFLS  G PC+ P+WG V+ ++L  N + W    GT RD++P +PLPF +G+P +GG
Sbjct: 653 RIQPFLSLVGFPCQAPSWGNVAGINLANNSIAWIHPNGTSRDNTPFIPLPFPVGVPAMGG 712

Query: 716 PVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTY-EVNGKQYVVIAAG 774
           P+ TAG V F+  T D YLRA+    G+ +W +RLPAGGQATPMT+   + +QY+V+  G
Sbjct: 713 PMTTAGGVAFLSGTLDQYLRAYDITNGKEIWSSRLPAGGQATPMTFWGKDNRQYIVLVVG 772

Query: 775 GHGSFGTKLGDYVIAYALPDQK 796
           GHGSFGTK+GDY+IAYALP  K
Sbjct: 773 GHGSFGTKMGDYIIAYALPKNK 794


Lambda     K      H
   0.319    0.137    0.433 

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: 2263
Number of extensions: 147
Number of successful extensions: 13
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: 796
Length of database: 803
Length adjustment: 41
Effective length of query: 755
Effective length of database: 762
Effective search space:   575310
Effective search space used:   575310
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 (21.7 bits)
S2: 55 (25.8 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