GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Pseudomonas stutzeri RCH2

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate GFF4212 Psest_4285 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

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



>FitnessBrowser__psRCH2:GFF4212
          Length = 452

 Score =  161 bits (408), Expect = 3e-44
 Identities = 123/414 (29%), Positives = 200/414 (48%), Gaps = 40/414 (9%)

Query: 26  VWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHY-AFNAAPHGPYLALMEQL 84
           +WD++G + +D + G+  +NLG+    +VEA   Q   L +Y  F    H P +AL + +
Sbjct: 43  LWDSEGHKILDAMAGLWCVNLGYGREELVEAATRQMRELPYYNLFFQTAHPPAVALAKAI 102

Query: 85  SQFVPVSYPLAGM----LTNSGAEAAENALKVAR------GATGKRAIIAFDGGFHGRTL 134
           +   P     AGM     T SG+EA +  L++ R      G   K+ +I    G+HG T+
Sbjct: 103 ADIAP-----AGMNHVFFTGSGSEANDTVLRMVRHYWAIKGQPAKKVVIGRWNGYHGSTI 157

Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHL--PYPSADTGVTC--EQALKAMDRLFS--VELAV 188
           A  +L G  A ++Q  G +PG + H+  PY   + G     E  ++  D+L    +E+  
Sbjct: 158 AGASLGGMKAMHEQSDGPIPG-IEHIDQPYWFGEGGDMSPEEFGVRIADQLEQKILEVGE 216

Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248
           + VAAFI EP+QG GG +     +   ++       IL I DE+  GFGRTG+ F     
Sbjct: 217 DKVAAFIAEPIQGAGGVIIPPETYWPRIKEILARYDILFIADEVICGFGRTGEWFGSDYY 276

Query: 249 GIEPDLLLLAKSIAGG-MPLGAVVGRKELMAALPKGG---LGGTYSGNPISCAAALASLA 304
           G+EPDL+ +AK +  G +P+G V+ R E++  L +GG    G TYSG+P++ A AL ++ 
Sbjct: 277 GLEPDLMPIAKGLTSGYIPMGGVIVRDEVVQTLNEGGEFYHGFTYSGHPVAAAVALENIR 336

Query: 305 QMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANAD------GS 358
            + +E +    + +    +    RW+     P +G   GVG +  +E             
Sbjct: 337 ILREEKIVERVKTKTAPYLQ--SRWQELLDHPLVGEARGVGLLGALELVKNKKTRERFAD 394

Query: 359 PAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
           P    L +  E     GL++   G     + +  PL I  E ++E +  +  CL
Sbjct: 395 PGVGMLCR--EHCFRNGLVMRAVGDT---MIISPPLVISEEQIDELIGKVRLCL 443


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: 479
Number of extensions: 26
Number of successful extensions: 5
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: 452
Length adjustment: 32
Effective length of query: 384
Effective length of database: 420
Effective search space:   161280
Effective search space used:   161280
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: 51 (24.3 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