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_3622 PP_3622 putative Isoquinoline 1-oxidoreductase, beta subunit

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



>FitnessBrowser__Putida:PP_3622
          Length = 751

 Score = 1257 bits (3252), Expect = 0.0
 Identities = 622/732 (84%), Positives = 673/732 (91%), Gaps = 4/732 (0%)

Query: 12  VNLSRRRFLASTAVGALVIGFGLPLGAGRVQAATSA----ERGTQVPAFLEIRPDGTVRL 67
           VNLSRRRFLA TAVGALV+GFGLP+G+ RVQAA +A    ERGTQVPAFLEIRPDGTVRL
Sbjct: 20  VNLSRRRFLAGTAVGALVLGFGLPMGSARVQAAAAAAATAERGTQVPAFLEIRPDGTVRL 79

Query: 68  LSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMS 127
           LSPFMEGGQG  TAMAQIVGEELD DPA F+V++APPGEAYVVMENG+RITGGSMSVRMS
Sbjct: 80  LSPFMEGGQGPFTAMAQIVGEELDVDPAHFVVDSAPPGEAYVVMENGMRITGGSMSVRMS 139

Query: 128 YPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPV 187
           YPTMRRLGALAR MLLQAGA+  GVPV EL+T PG VVH  +GRS+ YGELA  A+D+PV
Sbjct: 140 YPTMRRLGALARGMLLQAGAEHLGVPVDELSTTPGNVVHTTTGRSVPYGELAGRAMDLPV 199

Query: 188 PDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTV 247
           PDPAS+ LRDPSQFRWIGKPV+RLDAYDKSTGKA Y ID+KVD MLHAAVQHAPRLGMTV
Sbjct: 200 PDPASVKLRDPSQFRWIGKPVRRLDAYDKSTGKAQYCIDIKVDGMLHAAVQHAPRLGMTV 259

Query: 248 GSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAADSALRVMPA 307
           GSLRN+ Q++ MKGVHSVH LPGAVAVVAERWWHAKRAVEAIQVDW+E AADS +R MPA
Sbjct: 260 GSLRNEDQIKAMKGVHSVHQLPGAVAVVAERWWHAKRAVEAIQVDWKEPAADSKVRPMPA 319

Query: 308 DFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALAR 367
           DFSSD  RE LA  QGP+RD+ENEGD+AGAL  AKT+VEA+YHNQYLNHAQLEPPSALAR
Sbjct: 320 DFSSDAWREHLATVQGPSRDEENEGDIAGALANAKTKVEASYHNQYLNHAQLEPPSALAR 379

Query: 368 FNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQA 427
           FNPDG+L++WLPNQAPDMFR DIA+RTGL+PAQI LHSPLLGGFFGRHFLYDSANPYPQA
Sbjct: 380 FNPDGSLDVWLPNQAPDMFRDDIARRTGLEPAQINLHSPLLGGFFGRHFLYDSANPYPQA 439

Query: 428 IALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEAL 487
           IALAKAV RP+KLIWSREEEFLRDVLRP+AVVKFRA LD  G+PVA+EAVSATEGPTEAL
Sbjct: 440 IALAKAVGRPVKLIWSREEEFLRDVLRPVAVVKFRAGLDADGMPVALEAVSATEGPTEAL 499

Query: 488 AGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDE 547
           AGKQG+KIDPTA+EGLSGKSYAI NKRIAQIYVKG  MLGYWRSVGNSLNDFFYESFLDE
Sbjct: 500 AGKQGEKIDPTALEGLSGKSYAIANKRIAQIYVKGPAMLGYWRSVGNSLNDFFYESFLDE 559

Query: 548 LADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPF 607
           LADKGG DP+ELRLHLLRDNPRLT LL A  +LSGGWKRGPFTAEDG++RARGVAMASPF
Sbjct: 560 LADKGGKDPFELRLHLLRDNPRLTNLLNAVADLSGGWKRGPFTAEDGSKRARGVAMASPF 619

Query: 608 GSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYV 667
           GS  A IAEVSI+NG+V+VHDIWQAIDPGSIVNPAI+E QVNGAVALGLSQTL+EEAVYV
Sbjct: 620 GSEAAVIAEVSIDNGQVRVHDIWQAIDPGSIVNPAIIEHQVNGAVALGLSQTLVEEAVYV 679

Query: 668 DGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQR 727
           DGKPRARNYDLYPIL P++MARVHVR++ESG KMGGIGEPPLPAVAPAVANAVAQLTGQR
Sbjct: 680 DGKPRARNYDLYPILPPSRMARVHVRIIESGAKMGGIGEPPLPAVAPAVANAVAQLTGQR 739

Query: 728 VRSLPLSRHTFS 739
           VRSLPLSRHTFS
Sbjct: 740 VRSLPLSRHTFS 751


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: 1843
Number of extensions: 81
Number of successful extensions: 2
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: 751
Length adjustment: 40
Effective length of query: 699
Effective length of database: 711
Effective search space:   496989
Effective search space used:   496989
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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
the source code
instructions for running GapMind on your computer

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