Alignments for a candidate for gdh in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdh in Phyllobacterium brassicacearum STM 196

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_106710215.1 CU102_RS06575 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_003010955.1:WP_106710215.1
          Length = 778

 Score =  828 bits (2138), Expect = 0.0
 Identities = 405/788 (51%), Positives = 530/788 (67%), Gaps = 21/788 (2%)

Query: 14  LTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYALLLLA 73
           LT L   L GA + +GG+WLA +GGSWYYI+   A L+T  LL+R+ S+A++VYA+L++ 
Sbjct: 5   LTALIFFLIGAALGVGGVWLAILGGSWYYILAAIAFLITCVLLFRKRSSAMLVYAILVVG 64

Query: 74  TLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYRGLYQPGKGALGAMG------VAL 127
           TL W +WE+G D+W LAPR  V+++ G+WL+ P+V RGL +    A  A G      VA+
Sbjct: 65  TLGWAIWEIGFDWWQLAPRGGVIMLLGLWLLTPWVRRGLNEEEDRAPSAWGPAIPLAVAV 124

Query: 128 VASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFSPLKQ 187
           +A+  V  YS+  DPQ + G L      AP+     N+ +GDW  Y R   G R+SPLKQ
Sbjct: 125 LAALGVAGYSMTQDPQQIVGELSKEVI-APEPDLGGNVPEGDWHQYGRTPYGQRYSPLKQ 183

Query: 188 INHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATGK 247
           I  +NV  LQVAWQ+QTGD+K P D GE T +VTP+K+RDTLYLCTPH    ALDAATGK
Sbjct: 184 ITPENVNTLQVAWQYQTGDVKLPDDVGETTYQVTPLKVRDTLYLCTPHNWAIALDAATGK 243

Query: 248 QKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDGRLFALDA 307
           +KWK+DP +  NP  QH TCRGVSY+  P        QP  C+ RIYLP +D RL ALDA
Sbjct: 244 EKWKYDPNVGLNPDRQHQTCRGVSYYADPTLTAG---QP--CAERIYLPTSDARLIALDA 298

Query: 308 ETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNFSTREPSGA 367
             G+ CP+FG+ G L L+   P    G Y  TSPPVI    I++ GAV DN+S  E SG 
Sbjct: 299 ANGQICPSFGDKGMLHLETGMPYNPAGYYYSTSPPVIAAGKIIVGGAVNDNYSIHEQSGV 358

Query: 368 IRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDIVYLPMGVTT 427
           IR FD+NTG L+W +D G  D      +  T+T NSPNSW+ +  D KL ++Y+P+G  T
Sbjct: 359 IRAFDINTGALIWNWDSGNPDVTTPLPEGQTYTHNSPNSWSVSSADEKLGLLYVPLGNQT 418

Query: 428 PDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLADITDKDGN 487
           PD  G  R+   E+++SS++AL+  +G++ W  QTVHHDLWDMD+P+QPTL DI    G 
Sbjct: 419 PDQLGAGRSENVEKFSSSIVALDLNSGQMRWVRQTVHHDLWDMDVPAQPTLLDINTATG- 477

Query: 488 TVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPYSELTFRPKQNL 547
            VP +  P K G+I+VL+RRTG+ ++P  E P P GA +GD  + TQP S LTF P + L
Sbjct: 478 AVPALVGPTKQGDIYVLNRRTGEPILPIEEVPAPTGAIEGDFTAPTQPVSGLTFMP-EPL 536

Query: 548 TDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEWGGISVDPHRQI 607
           T KDMWG +M+DQL CR+ F +LRYEG +TPPS QG+L++PGN G+F WG ++VDP RQ+
Sbjct: 537 TGKDMWGVSMFDQLACRIEFLKLRYEGRYTPPSLQGSLIYPGNFGVFNWGAVAVDPGRQV 596

Query: 608 AIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGVELNPFLSPFGL 667
               P  L F S+LIPR    P +  K       +E G+    G PY V + PF+SP GL
Sbjct: 597 MFGMPTYLAFTSRLIPRAEVPPPDNKK------ASEQGLNRNEGAPYAVVMGPFVSPLGL 650

Query: 668 PCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKMGMPMLGGPVATAGKVFFIG 727
           PC+ P WGYV+  DL+T ++ +  R GTVRDSSP+PLPFK+G+P +GGP+ TA  V F+G
Sbjct: 651 PCQAPPWGYVAGADLRTGKITYMHRNGTVRDSSPIPLPFKVGVPGIGGPMVTASGVAFLG 710

Query: 728 ATADNYLRAFSTDTGELLWQARLPAGGQATPMTYEV-NGKQYVVIAAGGHGSFGTKLGDY 786
           A  D+YLRA+   +G+ LWQARLPAGGQ+TPM++ + NGKQYVV+ AGGHGS GTK GDY
Sbjct: 711 AAVDDYLRAYDVTSGKQLWQARLPAGGQSTPMSFALENGKQYVVMVAGGHGSVGTKPGDY 770

Query: 787 VIAYALPD 794
           VIAY LP+
Sbjct: 771 VIAYTLPN 778


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: 2287
Number of extensions: 155
Number of successful extensions: 17
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: 778
Length adjustment: 41
Effective length of query: 755
Effective length of database: 737
Effective search space:   556435
Effective search space used:   556435
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 24 2021. The underlying query database was built on Sep 17 2021.

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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 2024 update 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