Alignments for a candidate for drdehyd-beta in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Cupriavidus basilensis 4G11

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate RR42_RS09125 RR42_RS09125 acylaldehyde oxidase

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



>FitnessBrowser__Cup4G11:RR42_RS09125
          Length = 755

 Score =  397 bits (1021), Expect = e-115
 Identities = 272/773 (35%), Positives = 396/773 (51%), Gaps = 74/773 (9%)

Query: 14  LSRRRFLASTAVGALVIGFGLPLGAGRVQAATSAER---GTQVP--AFLEIRPDGTVRLL 68
           + RR FL +   GA  +  G  +   R + ATS      GTQV    ++++  D TV ++
Sbjct: 1   MKRRAFLVAGIGGAGALLVGWSVLPPRQRLATSQPLPAVGTQVGLNGWVKVAADNTVTIM 60

Query: 69  SPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAY----VVMEN----------- 113
               E GQG HT +A ++ +ELDA+ A   VE AP  + Y    VV+E+           
Sbjct: 61  MCRSEMGQGVHTGLAMVLADELDANWAQVKVEHAPVDKIYNNLEVVVEDLPFRADDDGVA 120

Query: 114 ---------------GLRITGGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELT 158
                          G  +TGGS S+   +  MR  GA ARAML+ A A +W VP G   
Sbjct: 121 RHLAAWLTRKLMREIGEMVTGGSSSLNDLWNPMREAGASARAMLIGAAAARWNVPAGACR 180

Query: 159 TQPGRVVHAASGRSLGYGELASSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKST 218
            Q G+V+H  SG++  +GELA+ A  +P+  PA + L+ PS+F+ IGK ++R++A  K  
Sbjct: 181 AQDGKVLH-PSGKTATFGELAAQAGQLPL--PAKVALKTPSEFKLIGKDIRRIEAASKID 237

Query: 219 GKALYSIDLKVDNMLHAAVQHAPRLGMTVGSLRNQSQVEGMKGVHSVHVL------PGAV 272
           G A + ID+  + +L+A+V   P LG TV S  + +    M G+  V  +       G V
Sbjct: 238 GTARFGIDVLPEGLLYASVTMCPTLGGTVASF-DGAVAAAMPGIVKVLAVDAYNGGTGGV 296

Query: 273 AVVAERWWHAKRAVEAIQVDWQEAAADS------ALRVMPADFSSDKHREFLAAQQGPTR 326
           AV+A+  + A +A++A+++ W   AA S      + R+  A  +SD H  +         
Sbjct: 297 AVIADNAYRAMKALDAVKIVWNPGAAASLSSPEVSRRLAQALDASDGHAYY--------- 347

Query: 327 DDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMF 386
                GDV  ALK A   V A Y   YL H  +EP +   +   DG   +W+  Q P + 
Sbjct: 348 ---RHGDVDAALKSAAKPVSAEYSAPYLAHGAVEPINCTVQVR-DGAARVWVSTQLPGLA 403

Query: 387 RADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIALAKA-VSRPIKLIWSRE 445
           R  ++K  G+D  ++ +   L+GG FGR    D  +   QA A+A+A   RP++ IWSR 
Sbjct: 404 RRAVSKVLGIDADKVDVQPQLIGGAFGRRLEVDFIS---QAAAIARAGGGRPVQTIWSRV 460

Query: 446 EEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEA----LAGKQGDKIDPTAVE 501
           ++   D  RP  + +F+A LD  G  VA    SA++    A    L G  G  ID T  E
Sbjct: 461 QDTTHDFYRPACLSRFKAGLDGAGNLVAWHNTSASQAVVPAMLARLLGLPGLGIDKTTTE 520

Query: 502 GLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRL 561
           G   + Y  PN R+  + V     +G+WRSVG+S   FF ESF+DELA   G DP   R 
Sbjct: 521 GAFDRPYEWPNARVGHVIVDLPVPVGFWRSVGHSHQAFFTESFIDELAAAAGKDPVAFRA 580

Query: 562 HLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIEN 621
            LL  +PR   +L  A +   GW +      DG  RARGVA+   +GS  A +AEVS+  
Sbjct: 581 GLLARHPRHLAVLHMAAD-KAGWAKPLGKTADGAARARGVALHEAYGSIVAQVAEVSVAP 639

Query: 622 GK-VKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYP 680
            K V+VH +  AID G  VNP ++  Q+  A+  GLS  L EE   VDG+   + +  +P
Sbjct: 640 DKTVRVHRVVCAIDCGLPVNPNLIRQQMESAIIFGLSAALFEEITIVDGQVHQKTFGDFP 699

Query: 681 ILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733
           ++       +   ++ S +   G+GEP  P +APAVANA+  LTGQR+R+LPL
Sbjct: 700 VIFMNNCPAIETYIMPSQDHPQGVGEPGTPPIAPAVANALFALTGQRLRALPL 752


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: 1355
Number of extensions: 78
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 739
Length of database: 755
Length adjustment: 40
Effective length of query: 699
Effective length of database: 715
Effective search space:   499785
Effective search space used:   499785
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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