GapMind for catabolism of small carbon sources

 

Alignments 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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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