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_00328 H281DRAFT_00328 alcohol dehydrogenase (cytochrome c)

Query= BRENDA::D4P700
         (796 letters)



>FitnessBrowser__Burk376:H281DRAFT_00328
          Length = 575

 Score =  182 bits (462), Expect = 4e-50
 Identities = 188/671 (28%), Positives = 269/671 (40%), Gaps = 153/671 (22%)

Query: 122 AMGVALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTR 181
           A  VA V S +  T +  +D   V      T D    AQ     +D  W  Y R   G  
Sbjct: 15  ATSVAAVVSLSCATAAFADDYPAV------TYDRLSAAQ-----SDPGWLTYYRTYNGQA 63

Query: 182 FSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFAL 241
            SPLKQI+  NVK+L+  W +     K P+D  +   E TPI     L++ TP   ++A 
Sbjct: 64  HSPLKQIDTSNVKQLKQVWSY-----KFPADLQQ-GFEATPIVNGHYLFVTTPKDNVYAF 117

Query: 242 DAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDGR 301
           DAA+GKQ WKF+P L    +F+   C            D  N   AL  + +Y+ + +G 
Sbjct: 118 DAASGKQLWKFEPKLGAE-SFKTACC------------DVINRGVALYGKNVYVAMLNGE 164

Query: 302 LFALDAETGERCPAFGNNGELDLQHKQPVTTPGM-YEPTSPPVITDTTIVMAGAVTDNFS 360
           + ALDA+TG             L  ++ +  PG+ Y  +  P+  D  +V+ G+    + 
Sbjct: 165 VVALDAQTGS------------LAWRKTMFEPGVGYAFSLAPLAIDGALVV-GSAGGEYG 211

Query: 361 TREPSGAIRGFDVNTGKLLW----VFDPGAKDPNAIP--ADEHTFTMNSPNSWAPAVYDP 414
            R   G I   + + G +LW    V   G K  N  P    EH        +W    YD 
Sbjct: 212 AR---GFIAALNPDNGNVLWKRFTVPAAGEKGANTWPDGMQEH----GGAPAWLTGTYDA 264

Query: 415 KLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPS 474
               +Y   GV  P  W  +  P    Y+ S+LAL+  TG L W YQ   HD WD D  +
Sbjct: 265 ASRTLY--WGVGNPGPWLADLRPGDNLYSDSLLALDPKTGDLKWHYQYTKHDTWDYDGVN 322

Query: 475 QPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAP---ETPVPQGAAKGDHVS 531
            P LA+I  +D N   +I+A  + G    +DR TGK +   P    T V    A G  V 
Sbjct: 323 TPVLANIKYQDKNYDAIIHAD-RNGYFHAIDRGTGKLIYAKPFVKATSVTGYTADGVPVQ 381

Query: 532 ATQPYSELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNL 591
               Y      PK   T +                                     P  L
Sbjct: 382 DPSKY------PKTGTTIE-----------------------------------TCPSFL 400

Query: 592 GMFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYG 651
           G   W  +S DP RQ+AI                       P      S +   +    G
Sbjct: 401 GGKNWWSVSYDPDRQVAIV----------------------PALHACMSLSGKSVTYMEG 438

Query: 652 VPY---GVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKM 708
           +PY   G E+ P     G       +G + A+D+ T + +W                +  
Sbjct: 439 LPYLGEGFEIKPEPGSKG-------YGELQAIDVTTGKKMWS---------------YWS 476

Query: 709 GMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQA-RLPAGGQATPMTYEVNGKQ 767
            +P  GG   TA  + F G + D +L AF + TG++LW++ +L +G  A P  +EV+GK+
Sbjct: 477 KLPWNGGVATTASGLAFSG-SLDGHLYAFDSSTGKVLWKSPKLASGIVAQPSVFEVDGKE 535

Query: 768 YVVIAAGGHGS 778
           YV I AG  G+
Sbjct: 536 YVAILAGYGGA 546


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: 1559
Number of extensions: 120
Number of successful extensions: 16
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 9
Number of HSP's successfully gapped: 4
Length of query: 796
Length of database: 575
Length adjustment: 39
Effective length of query: 757
Effective length of database: 536
Effective search space:   405752
Effective search space used:   405752
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: 54 (25.4 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