GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Klebsiella michiganensis M5al

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate BWI76_RS16705 BWI76_RS16705 glucose dehydrogenase

Query= BRENDA::D4P700
         (796 letters)



>FitnessBrowser__Koxy:BWI76_RS16705
          Length = 801

 Score =  553 bits (1425), Expect = e-161
 Identities = 321/807 (39%), Positives = 451/807 (55%), Gaps = 38/807 (4%)

Query: 8   FSVVRFLTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVY 67
           F+V R L VL +   G F  + G  L ++GGS +Y++ G A LL A     R+   L   
Sbjct: 13  FTVYRLLFVLLSFGIGLFFTLWGGKLLSLGGSAWYLLAGLAYLLIAVGYLIRSRYVLPFA 72

Query: 68  ALLLLATLAWGVWEVGTDFWALAPRTDV---LVIFGVWLVLPFVYRGLYQPGKGALGAMG 124
            L  L TL W ++EV   +W L PR  V   +++  +WL      R   +  + A  +  
Sbjct: 73  ILTFLLTLCWALYEVQFSYWGLIPRLVVPALMLMLALWLAATLPMRPARR--RYANWSAS 130

Query: 125 VALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFSP 184
              +   A L  + +    + NG + A+ D  P     S+    +W  + RD  GTRF+P
Sbjct: 131 AIFLVLLATLVSAFYPHGAIHNGVVNASGDATPTLASKSD----NWAFFGRDASGTRFAP 186

Query: 185 LKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAA 244
             +I   NVK L+VAW + TG  +R +  G   DE TP++I DTLY CTP  ++ ALDA 
Sbjct: 187 YDEITPQNVKNLKVAWTYHTG--RRLTGAGIGVDENTPLQIGDTLYSCTPLNVVTALDAD 244

Query: 245 TGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDAS---NTQPAL--CSRRIYLPVND 299
           TGK +W+FDP   T    +HVTCRGV Y++  +    S      PAL  C +RI +   D
Sbjct: 245 TGKARWRFDPHAGTA---EHVTCRGVGYYDVQSDDSLSAEEKASPALLQCPQRILVSTVD 301

Query: 300 GRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGM-YEPTSPPVITDTTIVMAGAVTDN 358
            RL AL+A+TGE C  FG++G +DL+     T     Y PTS PVI     V+ G V D 
Sbjct: 302 ARLIALNAKTGEPCDDFGDHGSVDLKQGMDNTENSKRYHPTSTPVIMGHIAVLGGWVRD- 360

Query: 359 FSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDI 418
               EPSG +R FDV  G ++W +D G  +    P     +T+ +PN W    +D +L++
Sbjct: 361 IVHGEPSGVVRAFDVRNGNVVWAWDVGQPENVTDPVKGRVYTLETPNVWTVPGFDKELNL 420

Query: 419 VYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTL 478
           +YLP G   PD WGG+R   +E+Y SSV+A++A+TG+  W +QTVHHD+WD DLPSQP L
Sbjct: 421 IYLPTGNGPPDYWGGDRNAAKEKYGSSVVAVDASTGETKWVFQTVHHDIWDYDLPSQPVL 480

Query: 479 ADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPYSE 538
             + ++ G  VPV+    KTG I+VLDRRTGK V    E PV    A+G+H+SATQP+S 
Sbjct: 481 FHMKNERGEEVPVLIQTTKTGQIYVLDRRTGKPVTRVEERPVAHDGAEGEHLSATQPFS- 539

Query: 539 LTFRPK---QNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFE 595
            T  P+   + LT+K MWG T +DQL+CR+ FK   Y G +TPPSE+  + +P  LG   
Sbjct: 540 -TGMPQLGVEPLTEKSMWGVTPFDQLMCRIDFKESTYLGMYTPPSEKPYIEWPSLLGGMN 598

Query: 596 WGGISVDPHRQIAIANPMALPFVSKLIPR-GPGNPEEPPKGATGGSGTETGIQPQYGVPY 654
           WGGI++D        N M +P    L+ +      +       G  GT   ++PQ   PY
Sbjct: 599 WGGITIDERTGTLFVNDMRMPLRMSLVRKEDMAKYKVSTDEVPGFMGT---VRPQIAGPY 655

Query: 655 -GVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKM----G 709
            GV ++   S  G+PC  P +G +SA+DL T +++W+  +G+V D+ P+ L   M    G
Sbjct: 656 GGVRIDILQSALGVPCNTPPFGTMSAIDLNTRQLMWQVPMGSVEDTGPLGLKTHMHIPLG 715

Query: 710 MPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTYE--VNGKQ 767
           MP LGGP +TA  + F   T DNYLRA  + TG+ LW+ARLP G  A P+ Y+    GK+
Sbjct: 716 MPTLGGPTSTASGLVFFAGTQDNYLRALDSATGKELWRARLPVGAVAAPLIYKSPKTGKE 775

Query: 768 YVVIAAGGHGSFGTKLGDYVIAYALPD 794
           YVVI+AGG  S    +GD +IA+AL +
Sbjct: 776 YVVISAGG-ASHSPDVGDDIIAFALEE 801


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: 2190
Number of extensions: 140
Number of successful extensions: 16
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: 801
Length adjustment: 41
Effective length of query: 755
Effective length of database: 760
Effective search space:   573800
Effective search space used:   573800
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 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