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.

Links

Downloads

Related tools

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