GapMind for catabolism of small carbon sources

 

Aligments for a candidate for drdehyd-beta in Shewanella sp. ANA-3

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate 7024305 Shewana3_1497 aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead (RefSeq)

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



>lcl|FitnessBrowser__ANA3:7024305 Shewana3_1497 aldehyde oxidase and
           xanthine dehydrogenase, a/b hammerhead (RefSeq)
          Length = 748

 Score =  305 bits (782), Expect = 4e-87
 Identities = 242/762 (31%), Positives = 356/762 (46%), Gaps = 65/762 (8%)

Query: 13  NLSRRRFLASTAVGALVIGFGLPLGAGRVQ---AATSAERGTQVPAFLEIRPDGTVRLLS 69
           N+SRR  L     GA  +G GL LGA  +     A + ++  ++  F+ I  D  V L  
Sbjct: 9   NISRRDVLK--LFGA--VGGGLALGASGLSWSPMALAQDQQARLNLFIAIGEDDKVYLTC 64

Query: 70  PFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSYP 129
              E GQG  T + QI+ EEL+AD    +       + Y         T GS S+R +Y 
Sbjct: 65  HRSEMGQGIRTGILQILAEELEADWDKIVPIQGLADKRYASQN-----TDGSRSIRENYD 119

Query: 130 TMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPD 189
            MR +GA+AR ML QA A +W VPV E+  +  +V+HA SGR+  +GELA  A  +P+P 
Sbjct: 120 RMREMGAMARTMLEQAAAARWKVPVSEVQAKDHQVLHAKSGRAARFGELALDAAGLPLPT 179

Query: 190 PASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGS 249
             S+ L+    F+ IG   + +D     TGKA+Y  D++VDNML+A++   P LG  V S
Sbjct: 180 ADSLRLKAVKDFKQIGASRQIVDMQAMLTGKAVYGYDIQVDNMLYASIMRPPVLGSDVAS 239

Query: 250 LRNQSQVEGMKGVHSVHVLP-----------GAVAVVAERWWHAKRAVEAIQVDWQEAAA 298
           L + S    + GV  V+ LP           G VAVVA   W A +  +A+QV W ++A 
Sbjct: 240 L-DDSAARKVAGVVDVYRLPTSKGAPAFQALGGVAVVATNTWSALQGRKALQVSWTQSAN 298

Query: 299 DSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQ 358
            S         S    +E +   Q P +     GD   A     T ++A Y   YL H+ 
Sbjct: 299 SS-------HDSKTYLQELVDKVQAPGKVVRQVGDEVKAWPKDDT-LKAIYTVPYLIHSS 350

Query: 359 LEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLY 418
           +EPP A A     G  EIW   Q P   + ++A   G+    + ++  LLGG FGR    
Sbjct: 351 IEPPVATANVTEKG-CEIWASTQTPQSTQQNVAVALGIAEDAVKVNVTLLGGGFGRKSKP 409

Query: 419 DSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEA-- 476
           D +    +A  L+K   RP+K+ WSRE+E        ++   ++A  D    P A+ A  
Sbjct: 410 DFS---VEAALLSKQFKRPVKVSWSREDEIQNGYYHAISAQCYQALFDANNKPTALLART 466

Query: 477 --VSATEGPTEALAGKQGDKIDPTAVEGLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGN 534
              S +    E +    G ++D     G     +A+ N R   +       +G+ RSV N
Sbjct: 467 GFPSISSTFAEGVEYPSGGELD----LGFVDVPFALANLRYEAVKASAHSRIGWMRSVCN 522

Query: 535 SLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQA--AGELSGGWKRGPF--- 589
             + F   SF+DE+A K      ++   LL    R T   Q    G       R P    
Sbjct: 523 IQHGFGVGSFVDEMAHKAKLSCPDMWRSLLGQARRETFENQGFKYGNYGEDLTRHPVDVG 582

Query: 590 ---------------TAEDGTRRARGVAMASPFGSHTAAIAEVSI-ENGKVKVHDIWQAI 633
                            + G  +  G A+   F S  A    V + E+ ++KV +   AI
Sbjct: 583 RYLKVIEAVEQAQAKAPKAGKNQGWGFAVHRSFVSVVAVAMRVEVGEDKQLKVLNAIAAI 642

Query: 634 DPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVR 693
           D G++VNP  V+AQ  GA+  GLS  L+ E  Y  GK    N+  YP+L   Q+  + V 
Sbjct: 643 DAGTVVNPDRVKAQTEGAIVFGLSLALMGEISYQQGKVMQSNFHDYPLLRLPQVPEMEVI 702

Query: 694 VVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPLSR 735
           +++S     G+GEP +P VAP++ NA+   TG R+R LP+++
Sbjct: 703 IIDSDAPPAGVGEPGVPPVAPSLTNAIFAATGLRIRDLPVNK 744


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: 1179
Number of extensions: 71
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 739
Length of database: 748
Length adjustment: 40
Effective length of query: 699
Effective length of database: 708
Effective search space:   494892
Effective search space used:   494892
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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