GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Rhizorhabdus wittichii RW1

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_011951898.1 SWIT_RS05365 pyrroloquinoline quinone-dependent dehydrogenase

Query= BRENDA::D4P700
         (796 letters)



>NCBI__GCF_000016765.1:WP_011951898.1
          Length = 669

 Score =  477 bits (1228), Expect = e-139
 Identities = 268/640 (41%), Positives = 361/640 (56%), Gaps = 29/640 (4%)

Query: 166 ADGDWPAYARDQQGTRFSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEI--TDEVTPI 223
           AD  W  +     GTRF+P  QI   NV  L+VAW++ TG++ R  +  ++  T+E TPI
Sbjct: 45  ADTPWDQWGATAGGTRFTPAAQITPGNVAHLRVAWRYSTGELARRPEGMQVNSTNETTPI 104

Query: 224 KIRDTLYLCTPHQILFALDAATGKQKWKFDPGLKTNPTFQ---HVTCRGVSYHEFPAAKD 280
               +L  CTP   + ALD ATG++KW +D   K + +F+      CRGVS       +D
Sbjct: 105 LAAGSLITCTPFGRVIALDPATGREKWTYDA--KVDRSFKLPDQYICRGVSQW-----RD 157

Query: 281 ASNTQPA-LCSRRIYLPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPT 339
           A    PA +C+ RI L   D R+ ALDA TG  C  FG  G + +   + +   G  +  
Sbjct: 158 ARAADPAGMCATRIILATVDMRVIALDARTGRPCAGFGEGGTVRVDPGK-LHHVGEVKLA 216

Query: 340 SPPVITDTTIVMAGAVTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKD--PNAIPADEH 397
           +P  I    IV+  +V DN     P G IR FD  +G+ +W FDP  +   P+     + 
Sbjct: 217 APAAIVRDRIVIGTSVLDNVRANAPRGIIRAFDARSGREIWTFDPIPQQGGPDRDWMGDS 276

Query: 398 TFTMNSPNSWAPAVYDPKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLV 457
             T  + N W+    DP+LD+VYLP    +PD +GG R P   R+A+SV+AL+A TG+LV
Sbjct: 277 RRTTGAANVWSVISGDPELDMVYLPTSSASPDYYGGLR-PGDNRHANSVVALDAATGRLV 335

Query: 458 WSYQTVHHDLWDMDLPSQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPE 517
           W+ Q +HHD+WD D+P+QPTL DI D+ G  +P +  P K G +FV DRRTG  + P  E
Sbjct: 336 WARQLIHHDIWDYDIPAQPTLVDI-DRGGRRIPALVQPTKQGYVFVFDRRTGAPLFPIDE 394

Query: 518 TPVPQGAAKGDHVSATQPYSELTFRP--KQNLTDKDMWGATMYDQLVCRVIFKRLRYEGP 575
            PVPQG   G+ +S TQP   L  RP   Q +T    WG T +D+  CR +  R R EG 
Sbjct: 395 VPVPQGGVPGEWLSPTQPRPRLP-RPIVPQKITPDQAWGFTPWDKAKCRDLIARYRSEGL 453

Query: 576 FTPPSEQGTLVFPGNLGMFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKG 635
           FTP +E+GT+ +P   G   WG  ++DP RQ+   N   +  V +L  R PG       G
Sbjct: 454 FTPITERGTITYPAASGGANWGAGAIDPARQVFFINSSRVASVIRLRKRKPGG-----SG 508

Query: 636 ATGGSGTETGIQPQYGVPYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGT 695
               S TE  + P  G PY V+    LSPFG PC  P WG ++A+DLKT   +W   +GT
Sbjct: 509 TVQLSATED-VSPMAGTPYEVKREWLLSPFGAPCTPPPWGGLTAIDLKTGATLWDVPLGT 567

Query: 696 VRDSSPVPLPFK--MGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAG 753
           + D  P+PLPF   +G P +GGPVATAG V FI AT D +LRA    TG+ LW+ RLP G
Sbjct: 568 INDRLPIPLPFDVALGTPNIGGPVATAGGVLFIAATMDRHLRAIDMRTGKELWRDRLPGG 627

Query: 754 GQATPMTYEVNGKQYVVIAAGGHGSFGTKLGDYVIAYALP 793
            Q TPM+Y   G+QYVV+A+G H  F T   D ++AYALP
Sbjct: 628 SQTTPMSYMAGGRQYVVVASGQHMWFQTPRSDEIVAYALP 667


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: 1991
Number of extensions: 141
Number of successful extensions: 17
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 796
Length of database: 669
Length adjustment: 40
Effective length of query: 756
Effective length of database: 629
Effective search space:   475524
Effective search space used:   475524
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 Apr 09 2024. 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