GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ofob in Magnetospirillum magneticum AMB-1

Align 2-oxoacid:ferredoxin oxidoreductase 1, subunit beta; Short=OFOR1; EC 1.2.7.11 (characterized, see rationale)
to candidate WP_011384545.1 AMB_RS10845 2-oxoglutarate synthase

Query= uniprot:OFOB1_AERPE
         (318 letters)



>NCBI__GCF_000009985.1:WP_011384545.1
          Length = 279

 Score =  189 bits (480), Expect = 7e-53
 Identities = 92/229 (40%), Positives = 143/229 (62%), Gaps = 4/229 (1%)

Query: 2   ASRGVASYRTEVWSDWCPGCGDFGILAAMQKAFAELNLDPAQTVVVSGIGCSSKTPHFIN 61
           A+     ++++V   WCPGCGD+ +L+++ KAFA+L L P +T VVSGIGCSS+ P + N
Sbjct: 8   ATYAAKDFKSDVKPVWCPGCGDYAVLSSITKAFADLGLKPHETSVVSGIGCSSRIPAYTN 67

Query: 62  VNGVHTIHGRGIAFATGIKLANPQLKVIVNGGDGDLLGIGVAHFVALGRRNLDVTVLIHN 121
             G+H+IHGR +A   G+KLA P L V+V GGDGD   IG  HF+   RRN+D+T ++ +
Sbjct: 68  TYGIHSIHGRALAVGQGLKLARPDLTVMVAGGDGDGFSIGGNHFLHACRRNVDLTYIVMD 127

Query: 122 NKVYGLTKGQASPTLRRGEKVKSLPVP--NLQDAVNPIALAIASGYTFVARAYSLWVDHL 179
           N+VYG+TKGQ SPT        ++  P        +P+A+A+ASG  F+AR +S   +  
Sbjct: 128 NRVYGMTKGQPSPTTESDWDASAMAPPGGTGMTPFHPLAIALASGANFIARGFSGDPNGT 187

Query: 180 KEILKAAINHKGSAVIDVLQPCVTYNDIYTAEFYKDRLYKLEDDPSWDP 228
            +I+  AI H G + + ++ PC+T+ +      +K+ +  +  +P+ DP
Sbjct: 188 AQIIAEAIRHPGFSFVAIMSPCITFRE--EQRDWKNTMRNVNIEPTTDP 234


Lambda     K      H
   0.319    0.137    0.416 

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: 253
Number of extensions: 10
Number of successful extensions: 2
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: 318
Length of database: 279
Length adjustment: 26
Effective length of query: 292
Effective length of database: 253
Effective search space:    73876
Effective search space used:    73876
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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:

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