Alignments for a candidate for aldox-large in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Magnetospirillum magneticum AMB-1

Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate WP_011386063.1 AMB_RS18770 xanthine dehydrogenase family protein molybdopterin-binding subunit

Query= metacyc::MONOMER-18071
         (749 letters)



>NCBI__GCF_000009985.1:WP_011386063.1
          Length = 732

 Score =  360 bits (924), Expect = e-103
 Identities = 242/756 (32%), Positives = 371/756 (49%), Gaps = 44/756 (5%)

Query: 5   GKPVKRIYDDKFVTGRSTYVDDIRIPAL-YAGFVRSTYPHAIIKRIDVSDALKVNGIVAV 63
           G+   R+ D +F+TG   Y DDI +    Y   VRS  PHA +  +D   A  + G++ V
Sbjct: 7   GQSRTRVEDLRFLTGGGCYTDDINLTGQSYGMVVRSLLPHADVT-VDAVAARAMPGVLLV 65

Query: 64  FTAKEINPLLKGGIRPWPT-YIDIRSFRYSERKAFPENKVKYVGEPVAIVLGQDKYSVRD 122
            TA E   + + GI P    ++   +     R      + ++ GEP+A V+ +     RD
Sbjct: 66  LTAAE---MAEQGIGPMVCGFLPEDAVPRHPRPVIAGPRTRHAGEPLAFVVAETLAQARD 122

Query: 123 AIDKVVVEYEPLKPVIRMEEAEKDQVIIHEELKTNISYKIPFKAGEVDKAFSESDKVVRV 182
           A + V+V+Y PL                H+     +       A  V +AF+ + +VV +
Sbjct: 123 AAEAVLVDYHPLPATP------------HDAFVWEMG-----DASRVAEAFARAARVVEL 165

Query: 183 EAINERLIPNPMEPRGIVSR-FEAGTLSIWYSTQVPHYMRSEFARILGIPESKIKVSMPD 241
           + IN RL P  MEPR  ++R    G L +   +Q  H +R   A +LGI   ++ V  PD
Sbjct: 166 DLINNRLAPTAMEPRACLARPLPGGRLELTAGSQGVHEIRDRLAPVLGIAADRLDVITPD 225

Query: 242 VGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNVFTGEVAVKRDG 300
           VGG FG K+   PE+   + ++ IL RPV+WT  R+E  L+ +  R ++ T  +A+  +G
Sbjct: 226 VGGGFGLKISPFPEQAMALVAARILDRPVKWTGDRTESFLSDTHGRGHLSTARLALDAEG 285

Query: 301 TILGIKGKLLLDLGAYITVTAGIQPLIIPM-MIPGPYKIRNLDIESVAVYTNTPPITMYR 359
             LG++ + + DLGAYI+      P +    M+ G Y I        A++T+T P+  YR
Sbjct: 286 RFLGLQVETVADLGAYISNYGAFVPTLAGTGMLTGVYDIPAFHARVRAIHTHTTPVDAYR 345

Query: 360 GASRPEATYIIERIMSTVADELGLDDVSIREKNLVTE--LPYTNPFGLRYDSGDYVGLLR 417
           GA RPEA Y IER++   A + GL  V IR++N +     PY +     YDSG++  ++ 
Sbjct: 346 GAGRPEAAYCIERLVDAAAHDTGLSPVEIRKRNFIPPDAFPYASAGRHTYDSGEFARVMD 405

Query: 418 EGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGPWEYAEVRVDERGDVLVVTGT 477
             ++R G+ +      +   +G + G+GLAYY+EIC     E   + +   G   ++ GT
Sbjct: 406 RALERSGWADFASRQADSTARGRKRGIGLAYYIEICGGTSGEDVTLTLSPDGGAEILVGT 465

Query: 478 TPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAASMGTYGSRSVTIGGSAAIKVAE 537
             +GQG ETA AQ+VA  L + I RVRVI GDT  +    GT GSRS++  G A     E
Sbjct: 466 QSNGQGHETAYAQMVAAELGLAIERVRVIQGDTRRIGTGGGTGGSRSLSQQGGAIASAVE 525

Query: 538 KILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKMSWDDVASIAYRSHDPGLVEKII 597
             ++ ++  AA    +  +  +++ G ++              A +   +  P       
Sbjct: 526 SFIEHLQPQAARL--LQAERAEFDAGFYRAAGGSV------SFAQVLAEAETPLAASLRF 577

Query: 598 YENDVTFPYGVHIATVEVD-DTGVARVLEYRAYDDIGKVVNPALAEAQIHGGGVQAVGQA 656
                TFP G H+  VEVD +TG   ++ Y   DD+G V+NP L + QI GG VQ +GQA
Sbjct: 578 RPPAATFPNGCHVCEVEVDPETGETEIVRYTIVDDVGTVLNPLLLKGQIVGGAVQGIGQA 637

Query: 657 LYEQALLNENG--QLIVTYADYYVPTAVEAPK--FTSVFADQYHPSNYPTGSKGVGEAAL 712
           L E A+ +      L  +  DY VP A   P+  F++V   +     +P G KG GEA  
Sbjct: 638 LLEHAVFDPESTQPLTSSLIDYAVPRAAHIPEIDFSTV---EIPCRTHPLGLKGAGEAGT 694

Query: 713 IVGPAVIIRALEDAIGTRFTKTPTTPEEILRAIASK 748
           I     +I AL +A+  R    P TP  +  A+  K
Sbjct: 695 IGAAPAVINALCNALELRHMDMPATPLAVWNALNGK 730


Lambda     K      H
   0.317    0.136    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: 1279
Number of extensions: 71
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: 749
Length of database: 732
Length adjustment: 40
Effective length of query: 709
Effective length of database: 692
Effective search space:   490628
Effective search space used:   490628
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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