GapMind for Amino acid biosynthesis

 

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

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011386328.1 AMB_RS20110 histidinol-phosphate aminotransferase

Query= reanno::BFirm:BPHYT_RS14905
         (370 letters)



>NCBI__GCF_000009985.1:WP_011386328.1
          Length = 363

 Score =  239 bits (609), Expect = 1e-67
 Identities = 141/373 (37%), Positives = 209/373 (56%), Gaps = 14/373 (3%)

Query: 1   MTASFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAA 60
           MTA      +  I PY+ G+   E     G+D   I+KL+SNE  LG    A  A+   A
Sbjct: 1   MTAPAPRPGIMDIRPYVGGESAIE-----GVDR--ILKLSSNEGALGPSPKAMEALRAMA 53

Query: 61  SELGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSF 120
            E+ RYPD  A +L+ A+  R+G+ A  +  G GS+++L I   A+   G  ++Y+ + F
Sbjct: 54  PEMHRYPDGGAEDLRKAIGARFGLDASRIVCGAGSDELLGILCRAYAGPGDEVLYSAHGF 113

Query: 121 AVYALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEA 180
            +YA+A +  GA  +  P V    ++D +LAAV+  T+++F+ANPNNPTGT++   ++  
Sbjct: 114 LMYAIAAKACGATPVTAPEVDLTANVDNLLAAVTPRTKILFLANPNNPTGTYLPATEVAR 173

Query: 181 FLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAI 240
               +   +++V+D AYTE++ +      I  V    N++V RTFSK + L GLR+G+A 
Sbjct: 174 LRAGLRADILLVIDAAYTEFVSRNDYSGGIELVEAGDNVVVCRTFSKMYALGGLRLGWAY 233

Query: 241 AQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLE 300
               +  +LNRVR PFNV   A AA +AA ND A+ E   + N      L+    +LGL 
Sbjct: 234 CPENVAGVLNRVRNPFNVGAPALAAGLAAFNDTAYAELCKSHNDYWLPWLSGQLAELGLT 293

Query: 301 YVPSDGNFVLVR----VGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEEN 356
            VPS  NF+LVR     G D  A ++    L  +G+IVR +G YGL   LRITIG  EEN
Sbjct: 294 VVPSVCNFILVRFPKDAGKDAGAADKF---LRSKGIIVRAMGGYGLGDCLRITIGTGEEN 350

Query: 357 EAFIAALERTLAA 369
           +  +AAL+  + A
Sbjct: 351 QLVVAALKEFVGA 363


Lambda     K      H
   0.318    0.135    0.385 

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: 343
Number of extensions: 14
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: 370
Length of database: 363
Length adjustment: 30
Effective length of query: 340
Effective length of database: 333
Effective search space:   113220
Effective search space used:   113220
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: 49 (23.5 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