GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Pseudomonas putida KT2440

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate PP_0372 PP_0372 Acetylornithine aminotransferase 2

Query= curated2:Q89RB7
         (404 letters)



>FitnessBrowser__Putida:PP_0372
          Length = 426

 Score =  217 bits (552), Expect = 6e-61
 Identities = 136/372 (36%), Positives = 189/372 (50%), Gaps = 9/372 (2%)

Query: 26  VLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAFHNDQL 85
           V  RG+G W+WD +G+ YLD     +  S GH    ++ A+  QA  L      FHN  L
Sbjct: 45  VFVRGQGSWLWDNEGHAYLDFTQGGAVNSLGHSPSVLVKALGNQAQALINPGSGFHNRGL 104

Query: 86  APFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADNFHGR 145
                 +   TGS +   +NSGAEA E AIK  RKWG   +   +    II  +   HGR
Sbjct: 105 LGLVNRLCQSTGSDQAYLLNSGAEACEGAIKLARKWGQLHR---NGAYHIITASQACHGR 161

Query: 146 TLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAGVIIP 205
           +LG +  S DP       P  PGF  +PF D AAL   +   TVA ++EPIQGEAGVI  
Sbjct: 162 SLGALSAS-DPLPCNRCEPGLPGFSKVPFNDLAALHAEVDSRTVAIMLEPIQGEAGVIPA 220

Query: 206 PAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALAGGFYPV 265
              Y   V  LC    ++L+LDE+QTG+GR G LLAE+  G+ AD+  LGK L GG  P+
Sbjct: 221 TQEYLKGVETLCRELGILLILDEVQTGIGRCGALLAEELYGVRADIITLGKGLGGG-VPL 279

Query: 266 SAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLLEGLK 325
           +A+L+  +      PG+   +  GN L CA   A +  ++E G +      G  L EGL 
Sbjct: 280 AALLARGKAC-CAEPGELEGSHHGNALMCAAGLAVLDSVLEPGFLAQVQDNGRHLREGLS 338

Query: 326 DIRANTVR-EVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTIRIAPPLVIT 384
            +     + EVRG GL+ A++L  +   AR    A   +G+L        +R +P L ++
Sbjct: 339 RLTGRYGQGEVRGHGLLWALQL--KENLARELVAAALHEGLLLNAPQVDVVRFSPALTVS 396

Query: 385 SDEVDWALEQFA 396
              +D  L + A
Sbjct: 397 KGNIDEMLLRLA 408


Lambda     K      H
   0.319    0.136    0.405 

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: 511
Number of extensions: 29
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: 404
Length of database: 426
Length adjustment: 31
Effective length of query: 373
Effective length of database: 395
Effective search space:   147335
Effective search space used:   147335
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