GapMind for catabolism of small carbon sources

 

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

Align D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39) (characterized)
to candidate WP_043745229.1 AMB_RS18795 FAD-binding oxidoreductase

Query= BRENDA::Q8N465
         (521 letters)



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

 Score =  283 bits (724), Expect = 1e-80
 Identities = 178/467 (38%), Positives = 250/467 (53%), Gaps = 20/467 (4%)

Query: 67  LAAFERIV-PGGVVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCHERNLA 125
           L A   IV PG V+T+   L    V+     +G +  ++RP ++ EV+ ++R C    + 
Sbjct: 4   LHALSAIVGPGNVITEASDLAPYLVEERGLYQGAALGVVRPGSTAEVAEVVRLCAAAGIP 63

Query: 126 VNPQGGNTGMVGGSVPVFD--EIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRYVEE 183
           + PQGGNTG+ GG VP  D   +++ST R+ R+ +   V   L  +AGCVL  L +  EE
Sbjct: 64  MVPQGGNTGLCGGGVPSEDGQSVVISTERLTRIRAVDPVDFTLTAEAGCVLANLQQAAEE 123

Query: 184 RDFIMPLDLGAKGSCHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLR 243
              + PL LGA+GSC IGGN++TNAGG   LRYG+    VLGLEVVL DG V + L  LR
Sbjct: 124 AGCLFPLSLGAEGSCRIGGNISTNAGGTNVLRYGNTRDLVLGLEVVLPDGRVWNGLKRLR 183

Query: 244 KDNTGYDLKQLFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGML 303
           KDNTGY L+ LFIG+EGTLGI+T   +   P+PR +  AF+        L  FS  +   
Sbjct: 184 KDNTGYALQHLFIGAEGTLGIVTACVLKLFPRPREIATAFVALADLEAALPLFSRARTAS 243

Query: 304 GEILSAFEFMDAVCMQLVGRHLHLASPVQESPF------YVLIETSGSNAGHDAEKLGHF 357
           G+ ++A E +    ++L  RH+    P   +PF       +L+E S S  G   E L   
Sbjct: 244 GDSVTACELVPRRGLELGMRHV----PGVRAPFAAFHDWMLLLELSSSRPGGLREALEEM 299

Query: 358 LEHALGSGLVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKYDLSLPVERLYDIV-- 415
           L  A   GL  D  +A    +    W +RE I EA  ++G   K+D+++   R+ +++  
Sbjct: 300 LGQAFEDGLAVDAVIAESDAQRADFWRIREAIPEAQKKEGGSIKHDVAVATSRVPEMIRR 359

Query: 416 TDLRARLGPHAKHVVGYGHLGDGNLHLNVTAE--AFSPSLLAALEPH---VYEWTAGQQG 470
                        VV +GHLGDGN H N+T    A   + LA  E     V++     +G
Sbjct: 360 CTRAVEAAMPGVRVVPFGHLGDGNTHFNLTQPEGADKAAFLARWEEMNRIVHDIVVEMEG 419

Query: 471 SVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKALLDPKGILNPYKTL 517
           S+SAEHG+G  K D L + KP   L LM ++K  LDP G +NP K L
Sbjct: 420 SISAEHGIGRLKVDELAHYKPGVDLDLMARIKGALDPLGQMNPGKIL 466


Lambda     K      H
   0.321    0.139    0.426 

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: 698
Number of extensions: 39
Number of successful extensions: 5
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: 521
Length of database: 469
Length adjustment: 34
Effective length of query: 487
Effective length of database: 435
Effective search space:   211845
Effective search space used:   211845
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