Alignments for a candidate for drdehyd-beta in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Beijerinckia indica ATCC 9039

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate WP_012386272.1 BIND_RS17075 xanthine dehydrogenase family protein molybdopterin-binding subunit

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



>NCBI__GCF_000019845.1:WP_012386272.1
          Length = 775

 Score =  264 bits (674), Expect = 1e-74
 Identities = 239/784 (30%), Positives = 346/784 (44%), Gaps = 71/784 (9%)

Query: 1   MNLINELLDAPVNLSRRRFLASTAVGALVIGFGLPLGAGRVQAATSAERGTQVPAFLE-- 58
           M  +  + +A +  SRR FL + A  +L  GF    GA    A         V    E  
Sbjct: 1   MARLGSMQNAAMIQSRRSFLVTMAGASLAFGFTRGAGAAIDPATADGVPPNAVGTLFEPS 60

Query: 59  ----IRPDGTVRLLSPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENG 114
               I   GTV +     E GQ   TA+A+I+ +EL+AD  T  +        +     G
Sbjct: 61  LWYSIDSTGTVTVNIIRAEMGQHVGTALARILADELEADWKTVRITHVDTDPKW-----G 115

Query: 115 LRITGGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLG 174
           L +TGGS SV  ++P   R GA  R  L++AGA    V       + G+V   A  +S+ 
Sbjct: 116 LMVTGGSWSVSQTWPIFSRAGAAGRLALIEAGAALLKVAPSACVARDGKVY--AGTQSIA 173

Query: 175 YGELASSA---LDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDN 231
           YG++ +           D   +TL+  S+ R IGKPV  LD   K+ G+A+Y ID KV  
Sbjct: 174 YGDIIAQGPHFRQFSPEDLDKLTLKPVSERRLIGKPVTALDIPAKTNGEAVYGIDAKVPG 233

Query: 232 MLHAAVQHAP-RLGMTVGSLRNQSQVEGMKGVHSVHVL-------PGAVAVVAERWWHAK 283
           M+HA  +  P R G  V S+ + S    +KG     V+       PG V V+AE  + A 
Sbjct: 234 MVHARPKIPPTRYGSKVVSV-DDSAARKVKGYLQSLVIDDPSETVPGWVLVIAESTFAAM 292

Query: 284 RAVEAIQVDWQEAAADSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGA------ 337
           RA + ++V W            P    S+K  +  A +Q   RD+    ++ GA      
Sbjct: 293 RAADLVKVTWSAG---------PTAHISEKEIQDHAVEQIARRDNGVLLELGGAKGVDVA 343

Query: 338 ---LKGAKTQVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRT 394
               + A + +E TY    + H QLEP +ALA F  DG  EI   NQ   +    +AK  
Sbjct: 344 KPAFEAAASTLEQTYTTATVLHFQLEPLNALA-FEKDGIFEIHTGNQWQSLILPVLAKAL 402

Query: 395 GLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLR 454
                 I L S +LGG FGR    D A P   A   AKA+ RP+K++ +R+++ L D +R
Sbjct: 403 QRPQESIVLRSYMLGGGFGRRLNGDYAVP---AALAAKALGRPVKVVLTRQDDALFDSVR 459

Query: 455 PLAVVKFRAALDDKGLPVAIEAVSATEGPTEALA------GKQGDKIDPTAVEGLSGKSY 508
             +V   R A D       +E  +A   PTE +A      G++G   DP A+ G      
Sbjct: 460 SPSVQTVRMAFDAANKVTGMEHHAAAGWPTEVMAPAFMPKGQEGKPFDPFAIAGADHWYD 519

Query: 509 AIPN--KRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLHLLR- 565
             P   + ++          G+ RSVG    ++  ESF+DE A     DP   RL+LL  
Sbjct: 520 VGPQLVRALSNDLANATFRPGWLRSVGPGWINWALESFMDEAALHVKMDPLAFRLNLLNG 579

Query: 566 ----DNP-----------RLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSH 610
               DN            R   +++ A + +G  +  P     G   + G     P    
Sbjct: 580 KGQNDNAGSAPVSVGGASRQAEVIRRAAQRAGWGQALPADTALGLATSFGQEREMPTWMA 639

Query: 611 TAAIAEVSIENGKVKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGK 670
            AA   V  + G+V+V  +    D G+IV+P    AQ  GA   GLS  L E  ++  G+
Sbjct: 640 CAARVHVDRKTGQVRVEKLTIVTDAGTIVDPDGARAQTEGATLWGLSMALHEGTLFEKGQ 699

Query: 671 PRARNYDLYPILAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRS 730
            R  N D Y  L   +   + +  VES E   G+GEP    +APA+ NA+    G R+R 
Sbjct: 700 VRDTNLDTYTPLRIDETPELDISFVESTEMPVGLGEPATTVIAPAIGNAIFAAVGVRLRH 759

Query: 731 LPLS 734
           LP++
Sbjct: 760 LPIT 763


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: 1313
Number of extensions: 68
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: 775
Length adjustment: 40
Effective length of query: 699
Effective length of database: 735
Effective search space:   513765
Effective search space used:   513765
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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