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

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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Protein sequences (fasta format)
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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