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_0372 PP_0372 Acetylornithine aminotransferase 2

Query= BRENDA::O30508
         (406 letters)



>FitnessBrowser__Putida:PP_0372
          Length = 426

 Score =  249 bits (636), Expect = 1e-70
 Identities = 159/400 (39%), Positives = 221/400 (55%), Gaps = 10/400 (2%)

Query: 4   PHAQVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPAL 63
           PHA  +  +    ++P    AA + VRG+GS +WD  G   +DF  G AV SLGH+   L
Sbjct: 25  PHASEQSPE---RLMPGTERAAQVFVRGQGSWLWDNEGHAYLDFTQGGAVNSLGHSPSVL 81

Query: 64  VKALTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYA 123
           VKAL  QAQ + +  + F N   L L  +L  +T +++ +L NSGAEA E A KLAR++ 
Sbjct: 82  VKALGNQAQALINPGSGFHNRGLLGLVNRLCQSTGSDQAYLLNSGAEACEGAIKLARKWG 141

Query: 124 NDVYGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAI 183
             ++    Y II AS + HGR+L  ++    P   +   P   G + VP+NDL AL A +
Sbjct: 142 Q-LHRNGAYHIITASQACHGRSLGALSAS-DPLPCNRCEPGLPGFSKVPFNDLAALHAEV 199

Query: 184 SDKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMH 243
             +T A++LEPIQGE GV+PA Q YL+G   LC E   LL+ DEVQ+G+GR G L A   
Sbjct: 200 DSRTVAIMLEPIQGEAGVIPATQEYLKGVETLCRELGILLILDEVQTGIGRCGALLAEEL 259

Query: 244 YGVVPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVIN 303
           YGV  DI++  K LGGG P+ A+L  G+ A     G    ++ GN L  A   A LD + 
Sbjct: 260 YGVRADIITLGKGLGGGVPLAALLARGK-ACCAEPGELEGSHHGNALMCAAGLAVLDSVL 318

Query: 304 TPEVLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEK 363
            P  L  V+      +  L ++   YG   E+RG GLL    L +     AR+++ AA  
Sbjct: 319 EPGFLAQVQDNGRHLREGLSRLTGRYG-QGEVRGHGLLWALQLKE---NLARELVAAALH 374

Query: 364 EAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKL 403
           E +++     DVVRF+P+L +    IDE L R  RA A+L
Sbjct: 375 EGLLLNAPQVDVVRFSPALTVSKGNIDEMLLRLARAFARL 414


Lambda     K      H
   0.318    0.135    0.394 

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: 472
Number of extensions: 24
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: 406
Length of database: 426
Length adjustment: 31
Effective length of query: 375
Effective length of database: 395
Effective search space:   148125
Effective search space used:   148125
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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