GapMind for catabolism of small carbon sources

 

Aligments for a candidate for sdh in Pseudomonas putida KT2440

Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate PP_1444 PP_1444 quinoprotein glucose dehydrogenase

Query= BRENDA::Q70JN9
         (743 letters)



>lcl|FitnessBrowser__Putida:PP_1444 PP_1444 quinoprotein glucose
           dehydrogenase
          Length = 803

 Score =  469 bits (1207), Expect = e-136
 Identities = 262/671 (39%), Positives = 365/671 (54%), Gaps = 43/671 (6%)

Query: 91  DVPQMAPQQSASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPGQ 150
           D  +MA    A P  G+W AYG  +   RYSPL +ITPQNA +L+ A+   TG  P    
Sbjct: 155 DSSEMASAAPAMP-DGEWQAYGRTEHGDRYSPLRQITPQNAYRLEEAWRIRTGDLPTEND 213

Query: 151 TNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTA----ACK 206
             +   + TP+KV   LY C+A + ++ +DP TG EIWR++   K     +       C+
Sbjct: 214 PVELTNQNTPLKVNGMLYACTAHSRLLALDPDTGAEIWRYDPQVKSPTGTFKGFAHMTCR 273

Query: 207 GVTYFTS--------SQVPE--------GQPCHNRILEGTLDMRLIAVDAATGNLCEGFG 250
           GV+Y+          S  P+         Q C  R+   T D RLIA++A  G +CEGF 
Sbjct: 274 GVSYYDENRYVSRDGSPAPKITDAGQAVAQACPRRLYLPTADARLIAINADNGKVCEGFA 333

Query: 251 NGGQVNLMQGLGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGK 310
           N G ++L  G+G    G    T+P  +   +V++   V D +    PSGVIR YD   G 
Sbjct: 334 NQGVIDLTTGIGPFTAGGYYSTSPAAITRDLVIIGGHVTDNESTNEPSGVIRAYDVHDGH 393

Query: 311 FLWAWDVNRPNDHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSP 370
            +W WD N P+D         YSR + N W+  + D  LG++Y+P GN   D + A R+P
Sbjct: 394 LVWNWDSNNPDDTKPLAAGKMYSRNSANMWSIASVDEDLGMIYLPLGNQTPDQWGADRTP 453

Query: 371 EENKVSSAVVALDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTK 430
              K S+ VVALD+ TG  RW +Q  H D+WD D+GSQ TL+ +   DG   PA+I+PTK
Sbjct: 454 GAEKYSAGVVALDLATGKARWNYQFTHHDLWDMDVGSQPTLVHLKTDDGVK-PAIIVPTK 512

Query: 431 RGQTFVLDRRDGKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGM 490
           +G  +VLDRRDG PI+P+ E P P  G + GD  SPTQ  S     L  P+L E  MWG 
Sbjct: 513 QGSLYVLDRRDGTPIVPIREIPTPQ-GAVEGDHTSPTQARSD--LNLLGPELTEQAMWGA 569

Query: 491 SPIDQLFCRIKFRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNI 550
           +P DQ+ CRI+FR   Y G++TPPS ++  + YPG  G  +WGSVS DP   +L  + N 
Sbjct: 570 TPFDQMLCRIQFRELRYEGQYTPPS-EQGSLVYPGNVGVFNWGSVSVDPVRQLLFTSPNY 628

Query: 551 TPMYDQLVTRKKADELGLMPIDDPNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMC 610
                ++V R++  E      +    +P            G PY +++ PF     G+ C
Sbjct: 629 MAFVSKMVPREQVAEGSKRESETSGVQPN----------TGAPYAVIMHPFMSP-LGVPC 677

Query: 611 NRPPYGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVV 670
             P +G + AID+    KV+W+H  GT R + P  LP GLP  +G P+ GGS+VTAGGV 
Sbjct: 678 QAPAWGYVAAIDL-FTNKVVWKHKNGTTRDSTP--LPIGLP--VGVPSMGGSIVTAGGVG 732

Query: 671 FIAAATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEA-NGHQYVAIMAGGHHFMMTPV 729
           F++   D  +RA D + GK +W A LP GGQA PM+Y   +G QYV + AGGH  + T +
Sbjct: 733 FLSGTLDQYLRAYDVNNGKELWKARLPAGGQATPMSYTGKDGKQYVLVTAGGHGSLGTKM 792

Query: 730 SDQLVVYALPD 740
            D ++ Y L +
Sbjct: 793 GDYIIAYKLAE 803


Lambda     K      H
   0.315    0.134    0.428 

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: 2010
Number of extensions: 135
Number of successful extensions: 10
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: 743
Length of database: 803
Length adjustment: 41
Effective length of query: 702
Effective length of database: 762
Effective search space:   534924
Effective search space used:   534924
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 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 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