Aligments for a candidate for gdh in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources