GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Klebsiella michiganensis M5al

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate BWI76_RS24235 BWI76_RS24235 aminotransferase

Query= SwissProt::H3ZPL1
         (417 letters)



>FitnessBrowser__Koxy:BWI76_RS24235
          Length = 393

 Score =  297 bits (761), Expect = 3e-85
 Identities = 164/399 (41%), Positives = 246/399 (61%), Gaps = 12/399 (3%)

Query: 18  YEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAA 77
           +++  + +A  +K S +RELLK  +   VISL GG+PAPE F  E +    ++V+     
Sbjct: 2   HDRRLAARAGELKPSAVRELLKHSKLPGVISLGGGIPAPELFDTEGLNLAVQQVMNGRFN 61

Query: 78  QALQYGTTKGFTPLRLALAEWMRER-YDIPISKVDIMTTSGSQQALDLIGRVFINPGDII 136
            A QYG T+G+ PLR A++E  + R    P S V I  TSGSQQ+LD++ R  ++PGD I
Sbjct: 62  DAFQYGLTEGYPPLRQAVSELCQARGVACPASHVYI--TSGSQQSLDIVARTLLDPGDAI 119

Query: 137 VVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQ 196
           VVE PTYLAALQ F+  +   + +  DD+GM V+ L + L     E  +VK VY +PTF 
Sbjct: 120 VVERPTYLAALQVFQLAQANILSVDTDDDGMLVEQLADLL-----ETTRVKAVYLVPTFG 174

Query: 197 NPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEE----GRVIY 252
           NP G T++E RR+RL+ELA ++DF+I+ED+PYGE+ ++ E  +P+  +  E     +V+Y
Sbjct: 175 NPGGKTLSEARRRRLVELAKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVELGCEDQVVY 234

Query: 253 LGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIP 312
             TFSKILAPG RIGWI       ++  I KQ+ DL TN  SQVI  +Y+    L+  I 
Sbjct: 235 TSTFSKILAPGMRIGWIVMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIA 294

Query: 313 KIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAY 372
            I E Y+ +  A+  ALE  + + +++++P+GGMF+WA      DT   ++K +  GV Y
Sbjct: 295 LIREDYRKKCVALADALESQLGEHLEFSRPKGGMFLWARFRYPFDTMEWMKKTLENGVVY 354

Query: 373 VPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETI 411
           VPGEAF+       T+RL+++ V  + +   ++RLA+++
Sbjct: 355 VPGEAFYNDNPDTRTLRLSYSTVSADGLMTAVERLAKSL 393


Lambda     K      H
   0.318    0.137    0.398 

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: 423
Number of extensions: 17
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: 417
Length of database: 393
Length adjustment: 31
Effective length of query: 386
Effective length of database: 362
Effective search space:   139732
Effective search space used:   139732
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: 50 (23.9 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