Aligments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Aligments for a candidate for drdehyd-beta in Pseudomonas fluorescens FW300-N2E2

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate Pf6N2E2_1904 Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1904
          Length = 752

 Score = 1038 bits (2684), Expect = 0.0
 Identities = 512/732 (69%), Positives = 601/732 (82%), Gaps = 4/732 (0%)

Query: 11  PVNLSRRRFLASTA---VGALVIGFGLPLGAGRV-QAATSAERGTQVPAFLEIRPDGTVR 66
           PVN+SRRRFL ++A    GALVI FG+PLG  R  + A +   G +VPAFLEIRPD TVR
Sbjct: 19  PVNVSRRRFLQASAGVTAGALVISFGIPLGPLRAAERAQALPPGARVPAFLEIRPDNTVR 78

Query: 67  LLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRM 126
           L SPF+EGGQG  T MAQ+VGEELD DPA+F+VE A PG  + VME G+R TGGS S+R 
Sbjct: 79  LQSPFIEGGQGIFTGMAQVVGEELDIDPASFLVENAAPGNDFKVMEGGMRFTGGSRSMRA 138

Query: 127 SYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMP 186
           SY TMRRLGA AR MLLQA +  W VP+ +LTT+PGRV+HAAS RS+ YGELA   LD+P
Sbjct: 139 SYMTMRRLGASARLMLLQAASSHWKVPLAQLTTEPGRVIHAASNRSITYGELAPLTLDLP 198

Query: 187 VPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMT 246
           +PDP ++TLRDP+ FRWIGKPV+R+D YDKSTGKA Y+ID +V+ MLHAAVQHAPRLG+ 
Sbjct: 199 IPDPQTVTLRDPATFRWIGKPVQRIDVYDKSTGKAQYTIDTRVEGMLHAAVQHAPRLGLQ 258

Query: 247 VGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAADSALRVMP 306
           VG +RN+ Q+  +KGVHSVH L GAVAVVA+RWW AKRAVEA+QV+W E   DS +R MP
Sbjct: 259 VGLVRNEDQIRNLKGVHSVHRLEGAVAVVAQRWWVAKRAVEALQVEWTEPGGDSTVRYMP 318

Query: 307 ADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALA 366
           A+F +  + E L+       + E EGD+   L GAK  V ATYH QYLNHAQLEPPSALA
Sbjct: 319 ANFDTQAYAEQLSKTTDAGDEAEREGDLQQGLAGAKKVVSATYHTQYLNHAQLEPPSALA 378

Query: 367 RFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQ 426
           RF+ +G L++WLPNQAPD+F AD+AKRTGLDP++ITLHSPLLGGFFGRHFLY +A+PYPQ
Sbjct: 379 RFDAEGNLDLWLPNQAPDLFLADVAKRTGLDPSKITLHSPLLGGFFGRHFLYPNASPYPQ 438

Query: 427 AIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEA 486
           AI LA++  RPIK+IWSREEEFLRDVLRP AVV+FRA LD++G+PVA EA+SATEGPTE 
Sbjct: 439 AIQLAQSTGRPIKVIWSREEEFLRDVLRPSAVVRFRAGLDEQGMPVAFEAISATEGPTEG 498

Query: 487 LAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLD 546
           +A KQGDKIDPTAVEGL+GK YAI ++RIAQ+Y +   MLGYWRSVGNS+NDF YE+FLD
Sbjct: 499 IANKQGDKIDPTAVEGLAGKKYAIAHRRIAQLYSQTPVMLGYWRSVGNSINDFMYEAFLD 558

Query: 547 ELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASP 606
           E+AD GG DPYELR  LL+ N RL+ LL+   +LSGGWKRGPFTA+DGT+RARGVAMASP
Sbjct: 559 EVADAGGQDPYELRAKLLQGNERLSHLLKVVADLSGGWKRGPFTAQDGTKRARGVAMASP 618

Query: 607 FGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVY 666
           FG+ TA IAEVSI NG VKVHDIWQAIDPGSIVNPAI+EAQVN AVALGLSQTL+E+A+Y
Sbjct: 619 FGTETAVIAEVSISNGAVKVHDIWQAIDPGSIVNPAIIEAQVNSAVALGLSQTLVEQAIY 678

Query: 667 VDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQ 726
             G P ARNYDLY IL P  MARVHVRVVESG  MGGIGEPPLPAVAPAVANAV++LTGQ
Sbjct: 679 KGGTPVARNYDLYRILTPEMMARVHVRVVESGAPMGGIGEPPLPAVAPAVANAVSRLTGQ 738

Query: 727 RVRSLPLSRHTF 738
           R+RS+PLS++ F
Sbjct: 739 RIRSMPLSQYRF 750


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: 1645
Number of extensions: 62
Number of successful extensions: 4
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: 752
Length adjustment: 40
Effective length of query: 699
Effective length of database: 712
Effective search space:   497688
Effective search space used:   497688
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)
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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