Alignments for a candidate for drdehyd-beta in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Pseudomonas putida KT2440

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate PP_2478 PP_2478 putative Isoquinoline 1-oxidoreductase, beta subunit

Query= metacyc::MONOMER-20833
         (739 letters)



>FitnessBrowser__Putida:PP_2478
          Length = 730

 Score =  361 bits (926), Expect = e-104
 Identities = 248/744 (33%), Positives = 378/744 (50%), Gaps = 42/744 (5%)

Query: 9   DAPVNLSRRRFLAST--AVGALVIGFGLPLGAGRVQAATSAERGTQ-------VPAFLEI 59
           +  V++SRRR L  +  A+  LV+   LP    +  AA +A  G           AF+ I
Sbjct: 6   EVTVDMSRRRLLQGSGIALSGLVLSTWLPPLVAKSAAAEAAAAGRLGDHSAEGYGAFVRI 65

Query: 60  RPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEA-YVVMENGLRIT 118
            PDG V ++SP +E GQG  T +A +V EEL+      +++ APP  A Y       + T
Sbjct: 66  GPDGVVTVISPKIEMGQGAQTGIAMMVAEELEVPLDQVVIQEAPPNSALYTDSLMQFQAT 125

Query: 119 GGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGEL 178
           GGS S R+++  +RR GA AR +L+QA A QW V       Q G+V    +G    YG+L
Sbjct: 126 GGSTSTRVTWEPLRRAGATARILLIQAAALQWRVAPSLCHAQNGQVF-GPNGLQAAYGDL 184

Query: 179 ASSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQ 238
             +A  +P+PD  ++ L+ P QF+ +G   +RLD   K  GKA ++IDL++  ML A+  
Sbjct: 185 VEAAATLPLPD--AVPLKTPEQFKLLGTAAQRLDTPAKVNGKAHFTIDLQIPGMLVASSI 242

Query: 239 HAPRLGMTVGSLRN--QSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEA 296
             P  G   G L N   SQ   + GV  +  L  AVAV A  +W  ++A+ A++++W   
Sbjct: 243 TCPVYG---GRLLNVDDSQARRVPGVRDIVRLDNAVAVTASNFWTCQQAIRALKIEWD-- 297

Query: 297 AADSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNH 356
                L    A  S+   +E L A        +  GD+  A + + +Q EA Y    L+H
Sbjct: 298 -----LGPHAAIGSAQLDQELLVASSRDGVVAKRSGDIEQAKQQSASQFEAVYEQALLSH 352

Query: 357 AQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHF 416
           +  EP S +A    D   E+W+  Q P   +   A+ TGL   +I +H+ L+GG FGR  
Sbjct: 353 SPFEPMSCVAHVRKDAC-ELWVGTQVPVFAQQTAAQVTGLPVEKIQVHNQLIGGAFGRRL 411

Query: 417 LYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEA 476
            +D      QA+A+A+ V  PIKLIWSREE+   D+ RPL   + +AALD++G P+  E 
Sbjct: 412 EFDFIT---QAVAIARQVDYPIKLIWSREEDMTHDLYRPLYADRMQAALDEQGRPLGWEH 468

Query: 477 VSATEGPTEALAGK-QGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPML---GYWRSV 532
             A         G    + +D  AVE      Y++ + ++   Y++  P +    +WR V
Sbjct: 469 RIAGASILARYVGSLPPNGVDSDAVEVAVDPIYSLVHLQVR--YIRQEPSVVPVSWWRGV 526

Query: 533 GNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAE 592
           G     +  E F+DELA     DP   RL L+ + PR   +L+   E +  W + P  A 
Sbjct: 527 GPLRGTYALECFIDELAHNAKADPVAYRLELMAEQPRAQAVLRLLAEKTD-WNK-PLPAG 584

Query: 593 DGTRRARGVAMASPFGSHTAAIAEVSIENGK-VKVHDIWQAIDPGSIVNPAIVEAQVNGA 651
            G    RGVA+++ FGS+ A + E+ +     +++  +   +D G   NP  V+AQ+ G 
Sbjct: 585 QG----RGVAVSAVFGSYVATLVELEMHGDLGIRIKRLVSVVDCGFATNPTSVKAQIEGG 640

Query: 652 VALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPA 711
              GLS +L  E +  +G+ +  N+  Y  L  ++   V V ++ S E  GG+GE     
Sbjct: 641 TLFGLSASLFNEILIENGQVQQTNFHNYRQLRISEAPAVEVHLLPSLEAPGGVGEAGTAL 700

Query: 712 VAPAVANAVAQLTGQRVRSLPLSR 735
           + PA+ NA+   +GQR+R LPLSR
Sbjct: 701 IGPALVNALYAASGQRIRRLPLSR 724


Lambda     K      H
   0.317    0.134    0.394 

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: 1198
Number of extensions: 54
Number of successful extensions: 11
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: 739
Length of database: 730
Length adjustment: 40
Effective length of query: 699
Effective length of database: 690
Effective search space:   482310
Effective search space used:   482310
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: 41 (21.7 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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Protein sequences (fasta format)
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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 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

GapMind for catabolism of small carbon sources