GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ofoa in Desulfatibacillum aliphaticivorans DSM 15576

Align 2-oxoacid:ferredoxin oxidoreductase 2, subunit alpha; OFOR2; EC 1.2.7.11 (characterized)
to candidate WP_015947475.1 G491_RS0115625 2-oxoacid:acceptor oxidoreductase subunit alpha

Query= SwissProt::Q9YBX7
         (642 letters)



>NCBI__GCF_000429905.1:WP_015947475.1
          Length = 382

 Score =  172 bits (436), Expect = 2e-47
 Identities = 116/346 (33%), Positives = 176/346 (50%), Gaps = 21/346 (6%)

Query: 244 GNDLVAMGKIVGGLGVITYYPITPSSDEALYVEKHSYISIDGPLAEKLGYDKIAVAIVQM 303
           GN+    G +  G+     YPITPSS+            I   +A +L         +QM
Sbjct: 10  GNEACMEGALYAGVQFYAGYPITPSSE------------ITEGMAMRL--PATGGKFIQM 55

Query: 304 EDELASINAVLGAAAAGARASTTTSGPGFSLMNEAVSLAVEAEIPVVVTLWMRAGPSTGM 363
           EDE++SI A++GA+  G +  T TSGPGFSLM E +  A+ AEIP V+   MR GPSTG+
Sbjct: 56  EDEISSICAIVGASLTGHKVMTATSGPGFSLMQEGLGYAIMAEIPCVIVNVMRGGPSTGL 115

Query: 364 PTRTGQQDLLHSIFSGHGDAPKIVLASGDHVEAFYDAIKAFNWAEEFQTPVIHLLDKYLA 423
           PT   Q D++ + +  HGD   + L +  H + F   ++AFN AE ++TPVI LLD+ + 
Sbjct: 116 PTHGSQGDVMQARWGVHGDHSIVALTASSHQDVFEMTVEAFNIAETYRTPVILLLDETVG 175

Query: 424 SSMVSLAREDLDPSKVP-ITRGKLLDNPPADYRRYEVVEDGISPRARLGSATMV-ITGLE 481
                L  E  +P ++P + R +       +Y  Y   EDG  P +  G      +TGL 
Sbjct: 176 HMREKL--EIPEPGELPLVERLRTSVREGVNYHPYLPREDGRLPMSDFGDVHRYNVTGLY 233

Query: 482 HDEYGYATEDPVMREIMMFKRERKFKVIEERIPDEEKAVLHGDSEASVALVSFGSTKQPI 541
           HD +G+ T DP M   ++         IE R+    +   +   +A   LVS+G + +  
Sbjct: 234 HDMWGFPTADPKMVHDLI---RHLIDKIENRVNVLARYKEYYLDDAERVLVSYGCSARSA 290

Query: 542 LEALEMLRDEGVRARFAQVRLLYPFPGRLVEEMLEGVEKVIMVEQN 587
           L  ++  R  G R    +++ L+PFP  +V+   +G + VI+VE N
Sbjct: 291 LHVVKDRRLRGERLGLLELQTLWPFPADVVKHCCDGKKSVIVVEMN 336


Lambda     K      H
   0.318    0.135    0.380 

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: 562
Number of extensions: 31
Number of successful extensions: 4
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: 642
Length of database: 382
Length adjustment: 34
Effective length of query: 608
Effective length of database: 348
Effective search space:   211584
Effective search space used:   211584
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: 52 (24.6 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

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:

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