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_061531860.1 CAter10_RS00515 xanthine dehydrogenase family protein molybdopterin-binding subunit

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



>NCBI__GCF_001584165.1:WP_061531860.1
          Length = 726

 Score =  335 bits (860), Expect = 4e-96
 Identities = 241/736 (32%), Positives = 370/736 (50%), Gaps = 35/736 (4%)

Query: 11  PVNLSRRRFLASTAVGA--LVIGFGLPLGAGRVQAATSAERGTQVPAFLEIRPDGTVRLL 68
           P   SRR FL ++AV    LV+GF +P   G   A T+ ++     AFL + PD  V + 
Sbjct: 6   PSKNSRRTFLKASAVSGVGLVLGFYIPSLTGIASAQTATKKSYPPNAFLRVGPDNKVVIQ 65

Query: 69  SPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSY 128
              ++ GQGT TA+  ++ EELD D      E A   + +     G+++ GGS SV  +Y
Sbjct: 66  VSKVDIGQGTLTALPMLLAEELDCDWNNVHAELAKGEDVFRDTAFGMQMVGGSTSVAHTY 125

Query: 129 PTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVP 188
              R +GA AR+ML+ A AKQW V      T  G V+   +G+   YG +A++A+ +P P
Sbjct: 126 QQYREIGARARSMLVAAAAKQWKVDPAACKTAAG-VITGPTGQHTTYGAVANAAMQLPAP 184

Query: 189 DPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVG 248
           +  ++ L++P+QF  IGK   RLD   KSTG+  + ID+ +  M  A +  A   G  +G
Sbjct: 185 E--TVQLKNPAQFTIIGKATPRLDGAAKSTGQQKFGIDVDLPGMKVALLARAVPWGAKIG 242

Query: 249 SLRNQSQVEGMKGVHSVHVLPG-----AVAVVAERWWHAKRAVEAIQVDWQEAAADSALR 303
            L + S  + + GV  +  +PG     +V +VA+ +W AK+A +A++++W        + 
Sbjct: 243 KL-DDSAAKAIPGVRKIFTIPGIRGGQSVVIVADGYWIAKKARDALKIEWDA----KGIE 297

Query: 304 VMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPS 363
            + +D     +RE       P      + DV+ +L  A  ++EA +   YL H  +EP +
Sbjct: 298 RVSSDSLFAAYREAAMKPGTPAA----KADVS-SLATAPKKIEAVFEFPYLAHTPMEPLN 352

Query: 364 ALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANP 423
               F  D    +W  +Q   M R  IAK  G+   ++  ++ + GG FGR  L +S N 
Sbjct: 353 MTLHFTGD-ACTVWTGSQFQSMDRQAIAKVLGIAITKVDFNTMMAGGAFGRRALPESENA 411

Query: 424 YPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSA---- 479
              A         P+K+++SRE++      RP+ V + R   D  G   A + V A    
Sbjct: 412 VEAAYIAKVMRGTPVKVMYSREDDLHGGYYRPMHVHRVRIGYDASGKIAAWDHVIAGQSI 471

Query: 480 -TEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLND 538
            T  P E+   K G  +D T  EG+    YAIPN  ++   ++    + + RSVG+S N 
Sbjct: 472 LTGSPFESFLVKDG--VDGTMTEGVLESHYAIPNLALSVHNMQANVPVLWHRSVGHSHNG 529

Query: 539 FFYESFLDELADKGGHDPYELRLHLL-RDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRR 597
           +  E+ +DE+A   G DP E R  L  +   R +  L  A   SG  KR     E G   
Sbjct: 530 YVMETLIDEIARSVGRDPVEYRKALFAQPGGRSSQALDLAVTRSGYGKR---KLEAG--H 584

Query: 598 ARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLS 657
           A GVA+   F +  A +AEVS+++G+ +VH +   +     +NP  +EAQ+ G +  GLS
Sbjct: 585 AWGVAVHHAFDTSVAYVAEVSLKDGRPQVHRVTAGVHCNMAINPRTIEAQIQGGLVFGLS 644

Query: 658 QTLL-EEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAV 716
                 E    DG  +  N+  Y  +   Q   V V +V S +   G+GEPP+P +APA+
Sbjct: 645 SIQPGYEITLKDGVVQQSNFPDYMPVLMGQCPTVEVYLVPSADTPTGVGEPPVPPIAPAI 704

Query: 717 ANAVAQLTGQRVRSLP 732
           ANAVA LTG+R+R LP
Sbjct: 705 ANAVAALTGKRLRKLP 720


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: 1229
Number of extensions: 57
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: 726
Length adjustment: 40
Effective length of query: 699
Effective length of database: 686
Effective search space:   479514
Effective search space used:   479514
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