GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcD in Magnetospirillum magneticum AMB-1

Align glycolate oxidase subunit glcD (characterized)
to candidate WP_043745229.1 AMB_RS18795 FAD-binding oxidoreductase

Query= CharProtDB::CH_024646
         (499 letters)



>lcl|NCBI__GCF_000009985.1:WP_043745229.1 AMB_RS18795 FAD-binding
           oxidoreductase
          Length = 469

 Score =  161 bits (407), Expect = 5e-44
 Identities = 139/473 (29%), Positives = 219/473 (46%), Gaps = 32/473 (6%)

Query: 20  SVLMALREHVPGLEILHTDEEIIPYECDGLSAYRTRPLLVVLPKQMEQVTAILAVCHRLR 79
           S+L AL   V    ++    ++ PY  +    Y+   L VV P    +V  ++ +C    
Sbjct: 2   SILHALSAIVGPGNVITEASDLAPYLVEERGLYQGAALGVVRPGSTAEVAEVVRLCAAAG 61

Query: 80  VPVVTRGAGTGLSGGALPLEKGVLLVMA--RFKEILDINPVGRRARVQPGVRNLAISQAV 137
           +P+V +G  TGL GG +P E G  +V++  R   I  ++PV      + G     + QA 
Sbjct: 62  IPMVPQGGNTGLCGGGVPSEDGQSVVISTERLTRIRAVDPVDFTLTAEAGCVLANLQQAA 121

Query: 138 APHNLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKIEVQTLDGEALT-LGS 196
                 +     ++ +C IGGN++ NAGG + L+YG T   +L +EV   DG     L  
Sbjct: 122 EEAGCLFPLSLGAEGSCRIGGNISTNAGGTNVLRYGNTRDLVLGLEVVLPDGRVWNGLKR 181

Query: 197 DALDSPGFDLLALFTGSEGMLGVTTEVTVKLLPKP---PVARVLLASFDSV----EKAGL 249
              D+ G+ L  LF G+EG LG+ T   +KL P+P     A V LA  ++      +A  
Sbjct: 182 LRKDNTGYALQHLFIGAEGTLGIVTACVLKLFPRPREIATAFVALADLEAALPLFSRART 241

Query: 250 AVGD-IIANGIIPG-GLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVE-SDVQEDC 306
           A GD + A  ++P  GLE    L +R     + A +    + +LL EL       ++E  
Sbjct: 242 ASGDSVTACELVPRRGLE----LGMRHVPG-VRAPFAAFHDWMLLLELSSSRPGGLREAL 296

Query: 307 ERVNDILLKAG-ATDVRLAQDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRALPG 365
           E +     + G A D  +A+ +A+R  FW  R+ A P   +        D  +    +P 
Sbjct: 297 EEMLGQAFEDGLAVDAVIAESDAQRADFWRIRE-AIPEAQKKEGGSIKHDVAVATSRVPE 355

Query: 366 VLEGIARLSQQY--DLRVANVFHAGDGNMHPLILFDANEP------GEFARAEELGGKIL 417
           ++    R  +     +RV    H GDGN H    F+  +P         AR EE+   + 
Sbjct: 356 MIRRCTRAVEAAMPGVRVVPFGHLGDGNTH----FNLTQPEGADKAAFLARWEEMNRIVH 411

Query: 418 ELCVEVGGSISGEHGIGREKINQMCAQFNSDEITTFHAVKAAFDPDGLLNPGK 470
           ++ VE+ GSIS EHGIGR K++++       ++     +K A DP G +NPGK
Sbjct: 412 DIVVEMEGSISAEHGIGRLKVDELAHYKPGVDLDLMARIKGALDPLGQMNPGK 464


Lambda     K      H
   0.320    0.140    0.415 

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: 633
Number of extensions: 29
Number of successful extensions: 6
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: 499
Length of database: 469
Length adjustment: 34
Effective length of query: 465
Effective length of database: 435
Effective search space:   202275
Effective search space used:   202275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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