GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_1444
          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:

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