GapMind for Amino acid biosynthesis

 

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

Align Salicylate synthase; Chorismate mutase; CM; EC 5.4.99.5; Isochorismate synthase/isochorismate lyase; EC 4.2.99.21; EC 5.4.4.2; Mycobactin synthase protein (uncharacterized)
to candidate WP_011384218.1 AMB_RS09175 anthranilate synthase component I

Query= curated2:Q73XV3
         (450 letters)



>NCBI__GCF_000009985.1:WP_011384218.1
          Length = 506

 Score =  157 bits (397), Expect = 7e-43
 Identities = 98/259 (37%), Positives = 134/259 (51%), Gaps = 1/259 (0%)

Query: 184 PSNYRDRVASAVAEIAAGRYHKVILSRCLQVPFAVDFPSTYRLARRHNTPVRSFLLRLGG 243
           P +Y   V  A   IAAG   +V+LS+ L VPF +   S YR  RR N     F L LG 
Sbjct: 234 PEHYCRMVEKAQEYIAAGDIFQVVLSQRLAVPFRLPPFSLYRSLRRLNPSPFLFFLDLGE 293

Query: 244 IRAVGYSPELVAAVRHDGVVVTEPLAGTRAFGRGALHDRQARDDLESNSKEIVEHAISVR 303
            + VG SPE++  +R D V +  P+AGTR  G+    D +   DL ++ KE+ EH + + 
Sbjct: 294 FQLVGSSPEILVRLRDDKVTI-RPIAGTRRRGKTPAEDEELAADLLADPKELAEHLMLLD 352

Query: 304 SSLQEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMDALEALFPAVTAS 363
               ++  +A  GT  VT  MTV     V H+ S V G++    D MDAL A FPA T S
Sbjct: 353 LGRNDVGRVAAIGTVEVTKKMTVEYYSHVMHIVSNVEGKIREGCDAMDALMAGFPAGTTS 412

Query: 364 GIPKAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHDGKTWLRAGAGII 423
           G PK   +E I  L+   R  Y+GA+     +G +D  + LR     DG  +++AGAGI+
Sbjct: 413 GAPKIRAMEIIDELETERRSFYAGAIGYFDGNGNMDTCIALRTTLVKDGTMYVQAGAGIV 472

Query: 424 EESTPEREFEETCEKLSTL 442
            +S P  E EE   K   L
Sbjct: 473 ADSVPLSEHEECMNKARAL 491


Lambda     K      H
   0.318    0.135    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: 434
Number of extensions: 18
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: 450
Length of database: 506
Length adjustment: 33
Effective length of query: 417
Effective length of database: 473
Effective search space:   197241
Effective search space used:   197241
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: 51 (24.3 bits)

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

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