GapMind for Amino acid biosynthesis

 

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

Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA

Query= curated2:O28084
         (416 letters)



>NCBI__GCF_000009985.1:WP_011386009.1
          Length = 903

 Score =  115 bits (288), Expect = 5e-30
 Identities = 112/395 (28%), Positives = 156/395 (39%), Gaps = 78/395 (19%)

Query: 93  PPGEGIIHQIMVERYV-----KPG----DLAVGADSHTCTYGGIGAFSTGMGSTDVAVAI 143
           PPG GI+HQ+ +E        K G    D  VG DSHT     +G    G+G  +    +
Sbjct: 175 PPGIGIVHQVNLEFLARGVLEKDGITYPDTLVGTDSHTTMINALGVAGWGVGGIEAEAGM 234

Query: 144 ALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIGDLGVDGATYKALEFHGECAENMTV 203
                 F  P+   V L G LP+G  A D++L L   L       K +EF GE   ++ V
Sbjct: 235 LGQPLVFLTPDVVGVHLHGRLPEGATATDLVLFLTERLRRAKVVGKFVEFFGEGTRSLAV 294

Query: 204 EERLTIANMAVECGAKAGIFESDENTRKFLAELGREGDFREV-------------KADED 250
            +R TIANMA E GA  G F  D+ T ++L   GR     EV                 D
Sbjct: 295 PDRATIANMAPEYGATMGFFPVDKETVRYLEATGRTDSEIEVFRAYYSAQGLFGMPMPGD 354

Query: 251 AEYEKEIYMDVSSLVPVVSKP--------------------------------------- 271
            +Y + I  D+ S+ P ++ P                                       
Sbjct: 355 IDYSEVIEFDLGSVQPSIAGPKRPQDRLNLSDMRRAFTSLFSAPAKDDGYGRPAEALGRR 414

Query: 272 HNVDNVAEISEVEGTEVNQVYIGTCTNGRLSDLEVAARILK------GRKVKEGVRLIVV 325
           H V+  A  +++   +V    I +CTN     + +AA +L       G KV   V+  + 
Sbjct: 415 HRVETTA-AADIGHGDVLIAAITSCTNTSNPGVMLAAGLLARKAVALGLKVGPRVKTSLA 473

Query: 326 PASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPCVG--------IHQGILADGEVC--IS 375
           P SR V       GL+      G  V+  GC  C+G        + Q I AD  VC  + 
Sbjct: 474 PGSRVVTEYLAKAGLLGDLESLGFGVVAYGCTTCIGNSGPLMPDLEQAIAADDLVCAAVL 533

Query: 376 TQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIA 410
           + NRNF+ R+       FL SP    A A+ G IA
Sbjct: 534 SGNRNFEARIHPAIKANFLMSPPLVVAFAIAGRIA 568


Lambda     K      H
   0.318    0.136    0.391 

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: 828
Number of extensions: 42
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 416
Length of database: 903
Length adjustment: 37
Effective length of query: 379
Effective length of database: 866
Effective search space:   328214
Effective search space used:   328214
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: 53 (25.0 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