GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Sphingobium czechense LL01

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_066608672.1 V473_RS16930 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_001046645.1:WP_066608672.1
          Length = 778

 Score =  606 bits (1562), Expect = e-177
 Identities = 342/805 (42%), Positives = 461/805 (57%), Gaps = 54/805 (6%)

Query: 12  RFLTVLFA---VLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYA 68
           RFL + F     +TGA +   G  L  +GGS +Y+  G  M+  A L WRR S +++++ 
Sbjct: 3   RFLNIAFLSSLTITGASLAWLGGRLLLLGGSPWYLASGIVMVAVALLGWRRRSVSILLFW 62

Query: 69  LLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYR--GLYQPGKGA-LGAMGV 125
           L L A L W  WEVG D WALAPR  + +  G++++ PF  R  G  QP  GA L   G+
Sbjct: 63  LYLAANLGWATWEVGADGWALAPRIAMPMGLGLYMLTPFYRRHVGRMQPLPGARLLWPGL 122

Query: 126 ALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQ------PLSNIADGDWPAYARDQQG 179
           AL+ +  V               L   AD  P  +      P +   DGDW AY  D+ G
Sbjct: 123 ALILAGGV--------------GLAFWADRMPAPRSELWGPPPAQAGDGDWIAYGNDRGG 168

Query: 180 TRFSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITD-EVTPIKIRDTLYLCTPHQIL 238
           +RFSPL QI   NV  L+ AW ++TG +    D  + T  +V P+KI + LYLC  +  +
Sbjct: 169 SRFSPLAQITPANVGHLRPAWTYRTGKL---GDGKQGTAFQVNPLKIGNRLYLCAGNNDV 225

Query: 239 FALDAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVN 298
            ALD  TG+Q W+ +P       +  V CRGV+Y+  P A          C+ RIY    
Sbjct: 226 IALDPETGRQLWRHNPKTDLAGVYGLV-CRGVTYYRVPQANGP-------CAERIYTATL 277

Query: 299 DGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDN 358
           D RL ALDA TG  CP FG  G++DL+        G Y  TSPP +    +V+ G VTD 
Sbjct: 278 DARLIALDAATGRPCPGFGRGGQVDLRSGLGTVDKGYYFVTSPPALVRGRLVLGGWVTDG 337

Query: 359 FSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDI 418
               EPSG IR FD  +G   W FD G  D + +PA   TFT  +PNSWAP   D  L +
Sbjct: 338 QRIGEPSGVIRAFDAVSGDFAWAFDIGRPDDHGLPAPGATFTPGTPNSWAPMSSDESLGL 397

Query: 419 VYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTL 478
           VY P G  TPD +GG+RT   +R++SSV+AL+A TG + WS+QT HHDLWD D+P+QPTL
Sbjct: 398 VYAPTGNATPDYFGGHRTANDDRFSSSVIALDAATGAVRWSFQTTHHDLWDYDVPAQPTL 457

Query: 479 ADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPYSE 538
            D+       V  +  P K G IF+LDR TGK ++P  E PVPQGA  G+ ++ TQPYS 
Sbjct: 458 VDLP----GGVRGLIQPTKRGEIFLLDRATGKPILPVEERPVPQGAVAGERIAKTQPYS- 512

Query: 539 LTFRPK---QNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPS-EQGTLVFPGNLGMF 594
            T  P       T+K MWG T  DQ +CR+ F++ R++G  TP S E  T+ +PG LG  
Sbjct: 513 -TTMPSFGGPRPTEKGMWGLTPIDQAICRIRFRQARFDGDMTPLSTEHPTITWPGYLGGI 571

Query: 595 EWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPY 654
           +WGG+SVD  R + I N   +   ++LIPR   +            G   G   Q GVPY
Sbjct: 572 DWGGVSVDKLRGLMIVNNNQVGNYNRLIPRAEADRRGIKPMNAVHMGDVGGPAAQQGVPY 631

Query: 655 GVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPL----PFKMGM 710
             ++ PFLSP  +PC+QP +G ++AVD++T ++VW + +GT RDS P+ L    P  MG+
Sbjct: 632 AAQIAPFLSPLAIPCQQPPYGRINAVDIRTGKMVWSRTLGTSRDSGPLALPTLVPIPMGV 691

Query: 711 PMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTY--EVNGKQY 768
           P +GG VATA  + FIGAT ++  RAF T TG+LLW+ARLPAGG A+P +Y    +G+Q+
Sbjct: 692 PNIGGSVATASGLTFIGATQEHAFRAFDTATGQLLWKARLPAGGNASPSSYWSSASGRQF 751

Query: 769 VVIAAGGHGSFGTKLGDYVIAYALP 793
           +VIAAGGHG+  +   D ++AYALP
Sbjct: 752 IVIAAGGHGAMLSGSSDQLVAYALP 776


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: 2281
Number of extensions: 157
Number of successful extensions: 19
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: 778
Length adjustment: 41
Effective length of query: 755
Effective length of database: 737
Effective search space:   556435
Effective search space used:   556435
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