GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Paraburkholderia bryophila 376MFSha3.1

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate H281DRAFT_03298 H281DRAFT_03298 quinoprotein glucose dehydrogenase

Query= BRENDA::D4P700
         (796 letters)



>FitnessBrowser__Burk376:H281DRAFT_03298
          Length = 879

 Score =  578 bits (1490), Expect = e-169
 Identities = 281/509 (55%), Positives = 352/509 (69%), Gaps = 9/509 (1%)

Query: 287 ALCSRRIYLPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITD 346
           A C RRI+LP  D RL AL+A+TG+ C  FGNNG++DL+      TPG Y  TSPP +T 
Sbjct: 378 AECPRRIFLPTADARLIALNADTGQPCTHFGNNGQIDLRTNIGPFTPGGYYSTSPPAVTR 437

Query: 347 TTIVMAGAVTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNS 406
             ++++G VTDN ST EPSG  R FDV+ G L+W +D G  D         T+  NSPN 
Sbjct: 438 DLVIISGHVTDNESTNEPSGVTRAFDVHDGHLVWNWDAGNPDETQPITGNQTYVRNSPNM 497

Query: 407 WAPAVYDPKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHD 466
           W+    D KL +VYLP+G  TPD WGG RTP  E+ A+ V+AL+  TGK+ W+YQ  HHD
Sbjct: 498 WSVFSVDEKLGMVYLPLGNQTPDQWGGMRTPASEKVAAGVVALDLATGKMRWNYQFTHHD 557

Query: 467 LWDMDLPSQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAK 526
           LWDMD+  QP+L D+    G   P + A  K G+++VL+R TGK +VP  E PVPQGA  
Sbjct: 558 LWDMDVGGQPSLIDLQTPSG-VQPALIASTKQGSLYVLNRETGKPIVPITEEPVPQGAGT 616

Query: 527 GDHVSATQPYSELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLV 586
           GDH S TQP+S L F+P + + ++DMWG   +DQL CRV FK LRY+G FTPPSEQG+LV
Sbjct: 617 GDHTSPTQPFSALNFKPPK-VRERDMWGTNPFDQLWCRVKFKSLRYDGMFTPPSEQGSLV 675

Query: 587 FPGNLGMFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTET-G 645
           FPGN G+F+WGGI+VDP RQI IANP  + F SKL+PR      + P       G+ET G
Sbjct: 676 FPGNFGVFDWGGIAVDPVRQILIANPSYMAFTSKLVPR-----SQIPSDNGEKKGSETSG 730

Query: 646 IQPQYGVPYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLP 705
           I+   G PYG ELN FLSP G+PC+ P WGYV+ VDL+TN +VW+ + GT+RDS+P+P+P
Sbjct: 731 IKLARGTPYGFELNAFLSPLGIPCQAPPWGYVAGVDLRTNHIVWEHKNGTIRDSAPLPIP 790

Query: 706 FKMGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTY-EVN 764
             +G+P LGG + TAG V F+  T D YLRA+   TG+ LWQARLPAGGQATPMTY + N
Sbjct: 791 MPLGVPSLGGMITTAGGVAFLSGTLDYYLRAYDVRTGDRLWQARLPAGGQATPMTYADSN 850

Query: 765 GKQYVVIAAGGHGSFGTKLGDYVIAYALP 793
           GKQYV++ AGGHGS GTK GDYVIAY LP
Sbjct: 851 GKQYVLVTAGGHGSLGTKQGDYVIAYTLP 879



 Score =  208 bits (529), Expect = 1e-57
 Identities = 114/266 (42%), Positives = 158/266 (59%), Gaps = 14/266 (5%)

Query: 20  VLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYALLLLATLAWGV 79
           ++ G  +  GG+ L  +GGSWYY++ G A+ LT  LL  R  +AL ++AL+L  +  W V
Sbjct: 19  IIIGLALAGGGVPLVALGGSWYYVVTGIAIALTGVLLSIRRRSALWLFALILFGSTIWAV 78

Query: 80  WEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGKGALGAMGVALVASAAVLTY--- 136
            E   DFW L PR  V ++  +WL+LP V R L   G  A    GV  + +A +LT    
Sbjct: 79  VEARFDFWQLLPRLWVWLVLALWLLLPPVTRKLVF-GPPAAHREGVVPLTAAVILTVLLG 137

Query: 137 --SVFNDPQVVNGALPATADNAPQAQPLSNIAD---GDWPAYARDQQGTRFSPLKQINHD 191
             + FN P    G L +TA  AP   P++  A+    DW  Y     G R+SPL QI  +
Sbjct: 138 LVTAFNHPYDRAGTLASTA--APPTTPIAGDANRQAADWTDYGGSPLGQRYSPLTQITPE 195

Query: 192 NVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATGKQKWK 251
           N  +L+VAWQF+TGD   P DP E TDE TPIK+ + L+LCTPH I+ ALD A+GK+ W+
Sbjct: 196 NAGQLKVAWQFETGDKPGPGDPTETTDENTPIKVGNKLFLCTPHSIVIALDPASGKELWR 255

Query: 252 FDPGLKTNPTF---QHVTCRGVSYHE 274
           +DP +++   F   +H+TCRGVSYH+
Sbjct: 256 YDPHIQSPVGFKHWEHMTCRGVSYHD 281



 Score = 28.5 bits (62), Expect = 0.002
 Identities = 23/75 (30%), Positives = 31/75 (41%), Gaps = 16/75 (21%)

Query: 240 ALDAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKD---ASNTQPALCSRRIYLP 296
           ALD ATGK +W +         F H     +     P+  D    S  QPAL +      
Sbjct: 539 ALDLATGKMRWNYQ--------FTHHDLWDMDVGGQPSLIDLQTPSGVQPALIA-----S 585

Query: 297 VNDGRLFALDAETGE 311
              G L+ L+ ETG+
Sbjct: 586 TKQGSLYVLNRETGK 600


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: 2638
Number of extensions: 190
Number of successful extensions: 13
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 6
Number of HSP's successfully gapped: 3
Length of query: 796
Length of database: 879
Length adjustment: 42
Effective length of query: 754
Effective length of database: 837
Effective search space:   631098
Effective search space used:   631098
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.

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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