Alignments for a candidate for drdehyd-beta in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Dyella japonica UNC79MFTsu3.2

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate N515DRAFT_2296 N515DRAFT_2296 isoquinoline 1-oxidoreductase, beta subunit

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



>FitnessBrowser__Dyella79:N515DRAFT_2296
          Length = 756

 Score =  377 bits (968), Expect = e-108
 Identities = 263/744 (35%), Positives = 375/744 (50%), Gaps = 49/744 (6%)

Query: 11  PVNLSRRRFLASTAVGALVIGFGLPLGAGRVQAATSAERGTQVP--------AFLEIRPD 62
           P N SRR  L    +G LV+ F L LG G      +A +G            AF+ +  D
Sbjct: 14  PDNPSRREALK---LGGLVVAF-LWLGGGAKVLGRAAAQGPVAAGDAAFAPNAFIRVGTD 69

Query: 63  GTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPG-EAYVVMENGLRITGGS 121
           G V L+ P +E GQG ++  A ++ EE+D      +VE AP   + Y     G + TGGS
Sbjct: 70  GAVHLVMPSIEMGQGAYSGQATLLAEEMDLGLDQVVVEHAPANRKLYANPLLGEQATGGS 129

Query: 122 MSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASS 181
            ++R  + T+R+ GA ARA+L+ A A +W V   + T   G + H ASGRSLGYGE+A++
Sbjct: 130 TTIRFCWTTLRQAGAAARALLVGAAAAKWKVDPAQCTVARGVIRHEASGRSLGYGEVANA 189

Query: 182 ALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAP 241
           A  +PVPD   +  +D +QF  IGKP++R+D   K  G   + IDL+V +M  A V+  P
Sbjct: 190 AAQLPVPD--KVQEKDAAQFALIGKPLRRVDTAGKVDGSLQFGIDLRVPDMKVATVKACP 247

Query: 242 RLGMTVGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQEAAADSA 301
             G  + ++ + S+   + G  +V  +  AVA V E +W AK+A++A+ + W        
Sbjct: 248 TFGGKLVAV-DDSRARQVPGFVAVLKIDNAVAAVGEHFWAAKQALDALDITWDHGP---- 302

Query: 302 LRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQ-VEATYHNQYLNHAQLE 360
                A +S+++  + LA  +         G   G + G K + +EATY    L HA +E
Sbjct: 303 ----NAQYSTEQLFKDLA--EASKHGTPIPGKAVGNVDGVKGKALEATYQLPLLAHATME 356

Query: 361 PPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDS 420
           P +A+    PDG  +IW   Q P       AK TGL P  I +H+  +GG FGR    D 
Sbjct: 357 PQNAIVHVRPDG-CDIWTGTQVPARCVDVAAKLTGLKPESIVVHNQYMGGGFGRRLFED- 414

Query: 421 ANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPV------AI 474
             P  QA+A A+ VS P+K++W+REE+   D  RP    +  A L D G PV      A 
Sbjct: 415 --PVEQAVAFARQVSYPLKMVWTREEDIAHDRYRPAYYDRIAATLGDDGKPVAWTHRIAS 472

Query: 475 EAVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIY--VKGAPMLGYWRSV 532
            +V AT  P     GK G  +D  A+E  +   Y  PN ++  +   +     LG+WR V
Sbjct: 473 GSVLATFAP--GAMGKNG--MDSDAIECAADVPYEFPNMKVEWVRHDMPEGVHLGWWRGV 528

Query: 533 GNSLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAE 592
           G   N F  ESF+DELA   G DP   R   L+ NPR   +L  A E   GW +G   A 
Sbjct: 529 GPVHNVFVVESFMDELAHAAGKDPLVYRREQLQKNPRALGVLNLAAE-KAGWGKGSLPAR 587

Query: 593 DGTRRARGVAMASPFGSHTAAIAEVSIE-NGKVKVHDIWQAIDPGSIVNPAIVEAQVNGA 651
            G    RGVA+A+PFGS+   I E  +   G+VK+     A+D G  VNP  V AQV G 
Sbjct: 588 VG----RGVAVAAPFGSYLCVIVEAEVSPQGEVKLRRAVAAVDCGIAVNPNTVAAQVQGG 643

Query: 652 VALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPA 711
           +  G +  L        G     N++ Y ++   +   + V +V+S E  GGIGE     
Sbjct: 644 LIFGWTAALYNGITIKHGAVEQHNFNDYRMMRINETPALEVHLVDSKEAPGGIGETGTVM 703

Query: 712 VAPAVANAVAQLTGQRVRSLPLSR 735
             PA+ NA+   TG R+RS P+ R
Sbjct: 704 AFPALFNALFAATGVRLRSYPIDR 727


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: 1408
Number of extensions: 80
Number of successful extensions: 10
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: 756
Length adjustment: 40
Effective length of query: 699
Effective length of database: 716
Effective search space:   500484
Effective search space used:   500484
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
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