GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Cronobacter condimenti 1330

Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate WP_071884227.1 BN137_RS05740 glucose/quinate/shikimate family membrane-bound PQQ-dependent dehydrogenase

Query= CharProtDB::CH_002195
         (796 letters)



>NCBI__GCF_000319285.1:WP_071884227.1
          Length = 798

 Score = 1444 bits (3737), Expect = 0.0
 Identities = 673/798 (84%), Positives = 736/798 (92%), Gaps = 2/798 (0%)

Query: 1   MAINNTGSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRS 60
           MA       RLLV LTALFAAL GLYLL+GG WLV+IGGSWYYPIAG+ ML  AW+LW+ 
Sbjct: 1   MAETKKTQSRLLVILTALFAALSGLYLLVGGIWLVSIGGSWYYPIAGVGMLATAWLLWKR 60

Query: 61  KRAALWLYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGA 120
             AALWLYA +LLGTM WG+WEVGFDFWALTPR DILVFFG+WLILPFVWRRL  P+   
Sbjct: 61  NAAALWLYAIILLGTMAWGIWEVGFDFWALTPRCDILVFFGVWLILPFVWRRLHTPSRAG 120

Query: 121 VAALVVALLISGGILTWAGFNDPQEINGTLSADATPA--EAISPVADQDWPAYGRNQEGQ 178
           V AL+V+L+I+ G+L WAGFNDPQE+NGTLSAD+TPA       + D DWPAYGRNQEGQ
Sbjct: 121 VPALLVSLIITAGLLFWAGFNDPQEVNGTLSADSTPAAVNGSQDIPDGDWPAYGRNQEGQ 180

Query: 179 RFSPLKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFA 238
           R+SPLKQIN DNVH LKEAWVFRTGD+K PNDPGEITNEVTPIKVGDTL+LCTAHQRLFA
Sbjct: 181 RYSPLKQINTDNVHQLKEAWVFRTGDLKLPNDPGEITNEVTPIKVGDTLFLCTAHQRLFA 240

Query: 239 LDAASGKEKWHYDPELKTNESFQHVTCRGVSYHEAKAETASPEVMADCPRRIILPVNDGR 298
           +DAA+GKEKWH+DP+L TN +FQHVTCRGVSYHEA    ASP+V+ADCPRRIILPVNDGR
Sbjct: 241 VDAATGKEKWHFDPQLNTNPTFQHVTCRGVSYHEATTANASPDVVADCPRRIILPVNDGR 300

Query: 299 LIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTIVMAGSVTDNFST 358
           L A+NA+NGKLCE+FANKG+LNLQ+NMP T PG+YEPTSPPI+TDK IV+AG+VTDNFST
Sbjct: 301 LFAVNADNGKLCESFANKGILNLQTNMPVTTPGMYEPTSPPIVTDKVIVIAGAVTDNFST 360

Query: 359 RETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAPAAYDAKLDLVYL 418
           RE SGVIRGFD+NTG+LLWAFDPGAKDPNAIP+DEH F+ NSPNSWAPA+YDAKLD+VYL
Sbjct: 361 REPSGVIRGFDINTGKLLWAFDPGAKDPNAIPADEHHFSLNSPNSWAPASYDAKLDIVYL 420

Query: 419 PMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWDMDLPAQPTLADI 478
           PMGVTTPDIWGGNRTPEQERYAS+I+ALNA+TGKL WSYQTVHHDLWDMDLPAQPTLADI
Sbjct: 421 PMGVTTPDIWGGNRTPEQERYASAIVALNASTGKLVWSYQTVHHDLWDMDLPAQPTLADI 480

Query: 479 TVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTPTQPFSELSFR 538
           TV G+ VPVIYAPAKTGNIFVLDRRNG+LVVPAPEKPVPQGAAKGDYVTPTQPFS+LSFR
Sbjct: 481 TVKGETVPVIYAPAKTGNIFVLDRRNGKLVVPAPEKPVPQGAAKGDYVTPTQPFSDLSFR 540

Query: 539 PTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGNLGMFEWGGISVD 598
           P KDLSGADMWGATM+DQLVCRVMFH +RYEGIFTPPSEQGTLVFPGNLGMFEWGG++VD
Sbjct: 541 PKKDLSGADMWGATMYDQLVCRVMFHSLRYEGIFTPPSEQGTLVFPGNLGMFEWGGLAVD 600

Query: 599 PNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYGVPYGVTLNPFLS 658
           P+R+VAIANPMALPFVSKLIPRGPGNPMEQPKDA+GTG+ESGIQPQYGVP+GVTLNPFLS
Sbjct: 601 PHRQVAIANPMALPFVSKLIPRGPGNPMEQPKDAQGTGSESGIQPQYGVPFGVTLNPFLS 660

Query: 659 PFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFNMGMPMLGGPIST 718
           PFGLPCKQPAWGYISALDLKTNEVVWKKRIGTP+DSMPFPMP PVPFNMGMPMLGGPI+T
Sbjct: 661 PFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPRDSMPFPMPFPVPFNMGMPMLGGPITT 720

Query: 719 AGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYEVNGKQYVVISAGGHGSF 778
            GNVLFI ATADNYLRAYN++NGEKLW+ RLPAGGQATPMTYEVNGKQYVV+SAGGHGSF
Sbjct: 721 GGNVLFIGATADNYLRAYNVTNGEKLWEARLPAGGQATPMTYEVNGKQYVVLSAGGHGSF 780

Query: 779 GTKMGDYIVAYALPDDVK 796
           GTKMGDYIVAYALPDD K
Sbjct: 781 GTKMGDYIVAYALPDDAK 798


Lambda     K      H
   0.319    0.137    0.436 

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: 2725
Number of extensions: 152
Number of successful extensions: 4
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: 798
Length adjustment: 41
Effective length of query: 755
Effective length of database: 757
Effective search space:   571535
Effective search space used:   571535
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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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