GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pseudomonas putida KT2440

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate PP_4108 PP_4108 putative 4-aminobutyrate aminotransferase

Query= reanno::pseudo1_N1B4:Pf1N1B4_3440
         (406 letters)



>FitnessBrowser__Putida:PP_4108
          Length = 416

 Score =  194 bits (493), Expect = 4e-54
 Identities = 133/403 (33%), Positives = 201/403 (49%), Gaps = 38/403 (9%)

Query: 31  GAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVS-NVFTNEPALRL 89
           G  + VWD  G+  IDF GGI V  LGH +PA+V A+  QA +L H + N   + P L L
Sbjct: 21  GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80

Query: 90  AHKL---VDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTL 146
             +L   V  ++       NSGAEA E A K+AR        T K  I+A    FHGRTL
Sbjct: 81  MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGA------TGKRAIIAFDGGFHGRTL 134

Query: 147 FTVNVGGQ-SKYSDGFGPKITGITHVPY----------------NDLAALKAAVSDKTCA 189
            T+N+ G+ + Y    G     + H+PY                + L +++ AV D   A
Sbjct: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVED-VAA 193

Query: 190 VVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPD 249
            + EP+QGEGG L  + ++ Q  R  CD    L++ DE+Q+G GR+G+ FA+   G+ PD
Sbjct: 194 FIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253

Query: 250 ILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLN 309
           +L  AKS+ GG P+ A++  ++L   L  G  G TY GNP++CA A A +  +    +  
Sbjct: 254 LLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLAT 313

Query: 310 GVNAKHDKFKTRLEQIGEKYGL---FTEVRGLGLLLGCVLSDAWKGKA----KDIFNAAE 362
               +     +R E+  +  GL      + G+G + G   ++A    A      +  AA 
Sbjct: 314 WGERQEQAIVSRYER-WKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAAR 372

Query: 363 REGLMILQAGP--DVIRFAPSLVVEDADIDAGLDRFERAAAKL 403
             GL+++ +G    +IR    L +E   ++ GLD  E+  A+L
Sbjct: 373 ARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415


Lambda     K      H
   0.320    0.136    0.400 

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: 415
Number of extensions: 16
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: 406
Length of database: 416
Length adjustment: 31
Effective length of query: 375
Effective length of database: 385
Effective search space:   144375
Effective search space used:   144375
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