GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-beta in Collimonas arenae Ter10

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate WP_061533487.1 CAter10_RS11315 xanthine dehydrogenase family protein molybdopterin-binding subunit

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



>NCBI__GCF_001584165.1:WP_061533487.1
          Length = 709

 Score =  395 bits (1016), Expect = e-114
 Identities = 255/726 (35%), Positives = 384/726 (52%), Gaps = 33/726 (4%)

Query: 15  SRRRFLASTAV--GALVIGFGLPLGAGRVQAATSAERGTQVPAFLEIRPDGTVRLLSPFM 72
           +RR FL S+A+  G L +G  LP   G +  A +A       A++ I  D T+ L+S   
Sbjct: 4   TRRDFLKSSALAGGGLTLGIMLP---GFMDEALAAGTIYTPNAWVHIADDNTITLISARS 60

Query: 73  EGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSYPTMR 132
           E GQG +TA+  ++ EEL  D     V  APP   Y     G +ITGGS S+R  +  +R
Sbjct: 61  EMGQGVYTALPMLIAEELGVDVHKVKVAIAPPNAVYTNALLGAQITGGSTSIRDGWEKLR 120

Query: 133 RLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPDPAS 192
             GA AR ML+ A A +W V    L  + G +V+  +G+   +G LA +A  +PVP    
Sbjct: 121 IGGAQARIMLVSAAASKWHVDPAALRVENG-MVYGPNGKKASFGALAEAASKLPVPK--D 177

Query: 193 ITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGSLRN 252
           + L+DP  F+ +GK  KRLD   K  G A+Y ID+K+  M++A+++  P +G  V S  +
Sbjct: 178 VQLKDPKDFKIVGKATKRLDTPSKVNGSAVYGIDVKLPGMVYASLEQCPVIGGKVLSF-D 236

Query: 253 QSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQE---AAADSALRVMPADF 309
            S+   M GV  V  +   VAV A  +W AK+A E ++V W E   A  D+A  +M    
Sbjct: 237 ASKARAMPGVIDVVQIDDGVAVAANSYWRAKKAREQLKVQWDEGPVAKIDNAT-MMDGIR 295

Query: 310 SSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFN 369
           +++K+ + +  ++         GD A A++GA   ++  Y +Q L HA LEP +  A F 
Sbjct: 296 AAEKNAKIINIKK--------TGDAAKAMQGAAKVLKVEYQSQLLAHATLEPQNFTADFK 347

Query: 370 PDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIA 429
            DG   +    Q     + ++AK  G+ P  + + +  LGG FGR    D      QA  
Sbjct: 348 -DGKCRVIGSTQFQQGAQGNVAKALGIKPEDVDVQTTFLGGGFGRRLEVDFI---VQAAQ 403

Query: 430 LAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPTEALAG 489
           ++KAV +P+KL+W+RE++   D  RP+A+ +    LD  G PVA+     ++  T+   G
Sbjct: 404 ISKAVGKPVKLVWTREDDTTHDFYRPMALHRMAGGLDADGKPVALTFQLTSQSVTQRAFG 463

Query: 490 KQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELA 549
              D +DP   E  S   Y IPN     +        GYWRSV ++LN F  ESF+DE+A
Sbjct: 464 LPKDTLDPFMAEA-SVVGYGIPNMTQDLVIHDTGLRAGYWRSVSHALNAFANESFIDEMA 522

Query: 550 DKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGS 609
              G DPY  RL LL   PR   +L+ A + +G     P      +   RG+A+   + +
Sbjct: 523 AAAGKDPYAFRLSLLDQQPRFANVLKQAAQKAGWGTPLP------SGHFRGIALMEGYDT 576

Query: 610 HTAAIAEVSI-ENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVD 668
           + A +AE+S+ ++ ++KVH +    D G +VNP  VEAQ+  ++A GLS  L  +     
Sbjct: 577 YMAQVAEISMHDDNEIKVHRVVVVADLGHMVNPDTVEAQLQSSIAFGLSAALGGQITLEK 636

Query: 669 GKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRV 728
           G+ +  N+  YP++   +M ++ V +V S EK GGIGEP    + PAVANAV   TG+RV
Sbjct: 637 GRVQQSNFGDYPVVRMNEMPKIDVTLVASTEKPGGIGEPATALIGPAVANAVFAATGKRV 696

Query: 729 RSLPLS 734
           R +PL+
Sbjct: 697 RKMPLT 702


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: 1217
Number of extensions: 63
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: 709
Length adjustment: 40
Effective length of query: 699
Effective length of database: 669
Effective search space:   467631
Effective search space used:   467631
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 24 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