GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Herbaspirillum seropedicae SmR1

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__HerbieS:HSERO_RS05420
          Length = 426

 Score =  361 bits (927), Expect = e-104
 Identities = 188/391 (48%), Positives = 253/391 (64%), Gaps = 3/391 (0%)

Query: 23  NAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLALME 82
           NAE+WD +G+R+IDF  GI VLN GH +P +++A++AQ  + TH A+   P+  Y+ L E
Sbjct: 35  NAELWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFTHTAYQIVPYASYVELAE 94

Query: 83  QLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNLNGK 142
           ++++  P +YP      ++GAEA ENA+K+AR  TG+  +IAF GGFHGRT+  + L GK
Sbjct: 95  RINRLTPGNYPKKTAFFSTGAEAVENAIKIARAHTGRPGVIAFAGGFHGRTMMGMALTGK 154

Query: 143 VAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAFIFEPVQGE 202
           VAPYK   G  PG V+H PYPSA  G+T E AL+A+  LF  ++  + VAA I EPVQGE
Sbjct: 155 VAPYKLGFGPFPGDVFHAPYPSALHGITSEDALEAVKGLFKSDIEAKRVAAIILEPVQGE 214

Query: 203 GGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSIA 262
           GGF A    F + LR  CDE GIL+I DE+QSG+GRTG+ FA     + PDL+ +AKS+A
Sbjct: 215 GGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEHYDVLPDLMTMAKSLA 274

Query: 263 GGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATWGERQEQAI 322
           GGMPL AV GR E+M A   GGLGGTY+GNP++ A+ALA L  M +E L T G+R    +
Sbjct: 275 GGMPLSAVNGRAEIMDAPAPGGLGGTYAGNPLAIASALAVLDVMEEEQLVTRGQRLGDKL 334

Query: 323 VSRYERWKASGLSPYIGRLTGVGAMRGIEFAN-ADGSPAPAQLAKVMEAARARGLLLMPS 381
               +  ++S   P I  + GVGAM  +EFA+ A G P      KV + A   GLLL+  
Sbjct: 335 QEHLKELRSS--VPQIAEVRGVGAMVAVEFADPATGKPDAEYTKKVQQHALNNGLLLLTC 392

Query: 382 GKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
           G   ++IR L PLTI   V++E L IL + +
Sbjct: 393 GSYGNVIRFLFPLTIPDTVMDEALGILAKAI 423


Lambda     K      H
   0.320    0.137    0.402 

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: 548
Number of extensions: 17
Number of successful extensions: 3
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: 416
Length of database: 426
Length adjustment: 32
Effective length of query: 384
Effective length of database: 394
Effective search space:   151296
Effective search space used:   151296
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 (21.8 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