GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Pseudomonas simiae WCS417

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF5065 PS417_25950 acetylornithine aminotransferase

Query= BRENDA::O30508
         (406 letters)



>FitnessBrowser__WCS417:GFF5065
          Length = 420

 Score =  251 bits (641), Expect = 3e-71
 Identities = 150/388 (38%), Positives = 222/388 (57%), Gaps = 9/388 (2%)

Query: 17  MVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWH 76
           ++P  A    + VRG+GS +WD   R  +DF+ G A  SLGH+   L+KAL +Q Q + +
Sbjct: 28  LMPCVARPPHVFVRGQGSWLWDSDDRAYLDFSQGNAANSLGHSPQVLIKALADQTQALIN 87

Query: 77  VSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIA 136
             N   N   L LA +L   T +++ +L NSGAEA EAA KLAR++   ++    Y II+
Sbjct: 88  PGNGLHNRAQLNLAERLCHRTGSDQAYLLNSGAEAVEAAIKLARKWGQ-LHRGGAYRIIS 146

Query: 137 ASNSFHGRTLFTVNVG-GQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCAVVLEPI 195
           AS   HGR+   ++   G P+  + F P+  G +HVP+NDL AL AA+  +T A++LEPI
Sbjct: 147 ASAGSHGRSFAAMSASAGGPE--NRFEPQLPGFSHVPFNDLSALHAAVDAQTVAILLEPI 204

Query: 196 QGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAK 255
           QGE GV+PA + YL+G  +LC E   LL+ DEVQ+G+GR G L A   YGV  DI++  K
Sbjct: 205 QGEAGVIPATEHYLKGVERLCRELGILLILDEVQTGIGRCGTLLAEQQYGVRADIITLGK 264

Query: 256 SLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKH 315
            LGGG P+ A+L  G+ A    VG    T+ GN L ++   A L+ +     +D V+   
Sbjct: 265 GLGGGVPLAALLARGK-ACCFEVGELEGTHHGNALMASAGLAVLEAVLEHGFMDHVRESG 323

Query: 316 ERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASPDV 375
                 L ++   Y    ++RG GL+ G  L+D+    A  V+ AA  E +++    P+ 
Sbjct: 324 LYLGEGLARLAYRYD-HGQLRGHGLMWGLTLSDD---SADAVVKAALHEGLIINAPQPNC 379

Query: 376 VRFAPSLVIDDAEIDEGLERFERAVAKL 403
           +RF P+L +  + IDE L R  RA +++
Sbjct: 380 LRFTPALTVSKSNIDEMLLRLARAFSRV 407


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: 439
Number of extensions: 26
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: 406
Length of database: 420
Length adjustment: 31
Effective length of query: 375
Effective length of database: 389
Effective search space:   145875
Effective search space used:   145875
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 Sep 17 2021. The underlying query database was built on Sep 17 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