Alignments for a candidate for gdh in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Burkholderia phytofirmans PsJN

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate BPHYT_RS08325 BPHYT_RS08325 glucose dehydrogenase

Query= BRENDA::D4P700
         (796 letters)



>FitnessBrowser__BFirm:BPHYT_RS08325
          Length = 837

 Score = 1165 bits (3014), Expect = 0.0
 Identities = 574/841 (68%), Positives = 657/841 (78%), Gaps = 50/841 (5%)

Query: 1   MGKNSSSFSVVRFLTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRN 60
           M   S+S  V+  +T+LF VLT  ++LIGG WL ++GGS YY+I G A+L  A+LLWRR+
Sbjct: 1   MTSQSNSRGVIGVVTLLFTVLTALYLLIGGAWLLSVGGSAYYLITGVALLGVAWLLWRRS 60

Query: 61  SAALVVYALLLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGKGAL 120
             ALV+Y+L+L+ T  W + E G DFWALAPR+ VLVIFGVWL+L   +R + +   G +
Sbjct: 61  PTALVLYSLVLIGTAIWALMESGPDFWALAPRSGVLVIFGVWLLLLVSWRLVGERKLGVV 120

Query: 121 GAMGVALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGT 180
             + VALVA A VL Y+ FNDPQ VNG L A+A  A  A   S I   DWPAY R Q+GT
Sbjct: 121 SLV-VALVAWAGVLVYASFNDPQQVNGTLSASAP-ASGAGAGSGIDPADWPAYGRTQEGT 178

Query: 181 RFSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFA 240
           R+SPL+QI  +NVK+LQVAW F+TGDMK P+DP EITDEVTPIKI D LYLC+PHQILFA
Sbjct: 179 RYSPLQQITPENVKDLQVAWTFRTGDMKGPNDPVEITDEVTPIKIGDLLYLCSPHQILFA 238

Query: 241 LDAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEF------------------------- 275
           LDA TG  KWKFDP LK++P+FQHVTCRGVSY +                          
Sbjct: 239 LDAKTGTLKWKFDPRLKSDPSFQHVTCRGVSYVDLSAGATAAAPATAPASDATATAAAPA 298

Query: 276 ---------------------PAAKDASNTQPALCSRRIYLPVNDGRLFALDAETGERCP 314
                                PAA  AS+T  A C+RRIYLPVNDG L+ALDA TG+RC 
Sbjct: 299 SDTATAAAPASDTATATTTAAPAATPASDTT-ATCTRRIYLPVNDGHLYALDALTGQRCE 357

Query: 315 AFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNFSTREPSGAIRGFDVN 374
            F N+G+LDLQH QPVTT GMYEPTSP +IT   I++AG+V DNFS REPSG IRGFDV 
Sbjct: 358 GFANHGDLDLQHAQPVTTAGMYEPTSPSIITSKVIIVAGSVEDNFSNREPSGVIRGFDVR 417

Query: 375 TGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDIVYLPMGVTTPDIWGGN 434
           TG+LLW FDPGAKDPN IP     +T NSPNSWAPA YD KLDIVYLPMGVTTPDIWGGN
Sbjct: 418 TGELLWAFDPGAKDPNHIPGAGEHYTWNSPNSWAPAAYDAKLDIVYLPMGVTTPDIWGGN 477

Query: 435 RTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLADITDKDGNTVPVIYA 494
           RTPEQERYAS +LALNA+TGKL W YQT HHDLWDMD PSQPTLADIT KDG +VPV+YA
Sbjct: 478 RTPEQERYASGLLALNASTGKLAWFYQTAHHDLWDMDQPSQPTLADITGKDGQSVPVVYA 537

Query: 495 PAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPYSELTFRPKQNLTDKDMWG 554
           PAKTGN+FVLDRRTG  VVPAPETPVPQGAA GDHVS TQP+S+LT+RP + LTD DMWG
Sbjct: 538 PAKTGNLFVLDRRTGVPVVPAPETPVPQGAAPGDHVSPTQPFSQLTYRPSKKLTDADMWG 597

Query: 555 ATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEWGGISVDPHRQIAIANPMA 614
           ATMYDQLVCRV+F +LRYEG FTPPS QGTLVFPGNLGMFEWGGI+VD  RQIA+ANP+A
Sbjct: 598 ATMYDQLVCRVMFHKLRYEGTFTPPSLQGTLVFPGNLGMFEWGGIAVDTDRQIAVANPIA 657

Query: 615 LPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGVELNPFLSPFGLPCKQPAW 674
           LPFVS+LIPRGPGNP EP  GA  GSGTE+GIQPQYGVPYGV +N FLSPFGLPCKQPAW
Sbjct: 658 LPFVSRLIPRGPGNPLEPVPGAK-GSGTESGIQPQYGVPYGVVINAFLSPFGLPCKQPAW 716

Query: 675 GYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKMGMPMLGGPVATAGKVFFIGATADNYL 734
           GY+SA+DLKTNE+VWK+RIGTVRDSSP+PLPF+MGMPMLGGP+ TAG V FIGATADNY+
Sbjct: 717 GYISAIDLKTNEIVWKKRIGTVRDSSPIPLPFRMGMPMLGGPIVTAGGVAFIGATADNYI 776

Query: 735 RAFSTDTGELLWQARLPAGGQATPMTYEVNGKQYVVIAAGGHGSFGTKLGDYVIAYALPD 794
           R F  + G+ +W+ARLPAGGQATPM+Y +NG+QY+VIAAGGHGSFGTKLGDYVIAYALP 
Sbjct: 777 RGFDVNNGKQVWEARLPAGGQATPMSYSINGRQYLVIAAGGHGSFGTKLGDYVIAYALPQ 836

Query: 795 Q 795
           Q
Sbjct: 837 Q 837


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: 2636
Number of extensions: 160
Number of successful extensions: 15
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 6
Number of HSP's successfully gapped: 5
Length of query: 796
Length of database: 837
Length adjustment: 41
Effective length of query: 755
Effective length of database: 796
Effective search space:   600980
Effective search space used:   600980
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: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
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
the source code
instructions for running GapMind on your computer

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