GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-beta in Thermithiobacillus tepidarius DSM 3134

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate WP_028990044.1 G579_RS0109820 xanthine dehydrogenase family protein molybdopterin-binding subunit

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



>NCBI__GCF_000423825.1:WP_028990044.1
          Length = 723

 Score =  425 bits (1093), Expect = e-123
 Identities = 280/739 (37%), Positives = 394/739 (53%), Gaps = 36/739 (4%)

Query: 8   LDAPVNLSRRRFLASTAV--GALVIGFGLP------LGAGRVQAATSAERGTQVPAFLEI 59
           + A  +  RR FL  +A+  G L +G  LP          R +A   A +     A++ I
Sbjct: 1   MSARFDAGRRHFLKVSALVGGGLAVGVYLPGCDRRPSEPPRPKAGAPAAQRFAPNAWVRI 60

Query: 60  RPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITG 119
            PD  V ++    E GQG  T+M  +V EELDAD     +  AP   AY   + G++ TG
Sbjct: 61  TPDDMVTIVVDKSEMGQGVMTSMPMLVAEELDADWQRVKLVQAPADPAYRNPKIGIQATG 120

Query: 120 GSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELA 179
           GS SV  S+  +R+ GA ARAML+ A A++W V      T+ G+V+H  SGR   YGELA
Sbjct: 121 GSTSVSSSWEPLRQAGATARAMLVAAAAREWQVTPESCRTEKGKVLHPDSGRQARYGELA 180

Query: 180 SSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQH 239
           S A   P+P    + L+ P  F+ IGKP+ RLD   K  G A++ ID+KV +ML A V H
Sbjct: 181 SLAARQPLPQ--DVPLKSPKDFQLIGKPLARLDTPAKVDGSAVFGIDVKVPDMLIATVAH 238

Query: 240 APRLGMTVGSLRNQSQVEGMKGVHSVHVLPGAVAVVAERWWHAKRAVEAIQVDWQ---EA 296
            P  G  +    + +Q + + GV +V  +   +AVVA  +W A++ ++A+QV W     A
Sbjct: 239 CPVFGGKLAGY-DATQAKAIPGVRAVLPVESGIAVVARDYWTARKGLQAVQVQWDLGPNA 297

Query: 297 AADSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNH 356
             DSA          DK     A Q  P+    ++G+   AL  A   VEA Y   +  H
Sbjct: 298 KLDSA--------GIDKLLTQAAGQ--PSAVAHDQGNAEQALGDAAKTVEAVYQLPFAAH 347

Query: 357 AQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHF 416
           A +EP +  A    D   E+W+P Q+    +   AK TGL   Q+ +H+ LLGG FGR F
Sbjct: 348 ATMEPMNCTAHVRGD-ACEVWVPTQSQTGVQMTAAKITGLPQEQVIVHTTLLGGGFGRRF 406

Query: 417 LYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVA-IE 475
             D      +A+ L++AV  P+KLIW REE+   D  RP    + RA LD  G+PVA   
Sbjct: 407 EQDFV---AEAVQLSQAVGAPVKLIWPREEDMQHDFYRPAMYNQLRAGLDRDGMPVAWTH 463

Query: 476 AVSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNS 535
            ++     +  +  +  D IDP++VEG +   YAIPN  +  +       +G+WRSVGNS
Sbjct: 464 RLAGPSIMSRVMPQRVKDGIDPSSVEGAAELPYAIPNIHVDYVMKDTGVPVGFWRSVGNS 523

Query: 536 LNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGT 595
              F  ESFLDELA  GG DP  LR  LL D  R   +L+ A +   GW  G   A  G 
Sbjct: 524 HTAFVKESFLDELAAAGGKDPLALRRALLSDAAREREVLELAAD-KAGW-GGKLPAGHG- 580

Query: 596 RRARGVAMASPFGSHTAAIAEVSI-ENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVAL 654
              RG+A+   FGS+ A +AEVS+ ++G ++VH I  A+D G++VNP  V AQV  A+  
Sbjct: 581 ---RGLAVHKSFGSYAAQVAEVSVAKDGTLRVHRIVCALDCGTVVNPDTVRAQVESAIIY 637

Query: 655 GLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAP 714
           GL+ TL        G+ +  N++ YP+L   +   + V ++ S E   G+GEP +P VAP
Sbjct: 638 GLTATLKGPITLAGGRVQQSNFNDYPLLRLDETPLIEVHLLPSREPPSGVGEPAVPPVAP 697

Query: 715 AVANAVAQLTGQRVRSLPL 733
           AVANAV   TG+R+R LP+
Sbjct: 698 AVANAVFAATGKRIRHLPI 716


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: 85
Number of successful extensions: 9
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: 723
Length adjustment: 40
Effective length of query: 699
Effective length of database: 683
Effective search space:   477417
Effective search space used:   477417
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 Apr 09 2024. 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