GapMind for catabolism of small carbon sources

 

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

Align indolepyruvate ferredoxin oxidoreductase (subunit 1/2) (EC 1.2.7.8) (characterized)
to candidate WP_043744857.1 AMB_RS16330 indolepyruvate oxidoreductase

Query= BRENDA::Q6LZB5
         (188 letters)



>lcl|NCBI__GCF_000009985.1:WP_043744857.1 AMB_RS16330 indolepyruvate
           oxidoreductase
          Length = 206

 Score =  130 bits (326), Expect = 2e-35
 Identities = 73/188 (38%), Positives = 108/188 (57%), Gaps = 3/188 (1%)

Query: 2   NIVIAAVGGQGAVLASKILGTLAQNLGKDVKVSEVHGMSQRGGSVVAYVKFGEKVYSPVV 61
           NI++   GGQG + A++IL   A   G D K SEV GM+QRGG V ++V+FG++V+SPV+
Sbjct: 7   NILVCGTGGQGVMTAAEILSQAAMARGLDCKKSEVAGMAQRGGVVTSHVRFGKRVWSPVI 66

Query: 62  EKGTADIVLAFEMLEGARYVDYLKENGKLVVNTQKIDPMPVITGDVKYPSDLNEKFEKLN 121
             GTADI++AFE+ EG+R+ D L+  G  +VNT ++ P  V  G  KYP D   +     
Sbjct: 67  TPGTADILVAFEVAEGSRWADMLRPGGVAMVNTIRLVPPVVSAGLFKYPDDPVAQMRAAG 126

Query: 122 IGYVPVDALSIAKNAGTLKAVNVALIGVLAKNSNIKKEEWIKAIKDTVPEK---FLELNL 178
           +     DA +IA+  G L+ +N  ++G +A        E  + I     E+    +E+N 
Sbjct: 127 VTVYDFDAGAIARELGDLRLINTIMLGAIADYLPFPAAELEEQIVGRFRERKPAMVEVNQ 186

Query: 179 KAFEMGYD 186
           KAF  G D
Sbjct: 187 KAFAAGRD 194


Lambda     K      H
   0.315    0.135    0.370 

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: 88
Number of extensions: 3
Number of successful extensions: 1
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: 188
Length of database: 206
Length adjustment: 20
Effective length of query: 168
Effective length of database: 186
Effective search space:    31248
Effective search space used:    31248
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: 42 (22.0 bits)
S2: 45 (21.9 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, 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