GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Pseudomonas fluorescens GW456-L13

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate PfGW456L13_1971 Succinylornithine transaminase (EC 2.6.1.81)

Query= curated2:Q4A0N2
         (394 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971
          Length = 406

 Score =  256 bits (654), Expect = 8e-73
 Identities = 143/380 (37%), Positives = 213/380 (56%), Gaps = 9/380 (2%)

Query: 9   DKYSSKNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQR 68
           D+    NY+P      +G G++VWD      ID   G +V   GH HP ++ AL EQ+ +
Sbjct: 14  DQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVGALTEQANK 73

Query: 69  ITMVSRALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESS 128
           +  VS    ++   +   K+      E     N+G EA E A K+AR+   D        
Sbjct: 74  LWHVSNVFTNEPALRLAHKLVDATFAERAFFCNSGAEANEAAFKLARRVAFD--RYGSEK 131

Query: 129 SEIIAMNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAII 188
            EIIA   +FHGRTL ++++  Q  Y  GFGP +  I +  + D+  LK  ++++T A++
Sbjct: 132 YEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCAVV 191

Query: 189 LEPIQGEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIY 248
           LEPIQGEGGV      ++Q  R+LCNE+N LL+ DE+Q G+GRTG +FA +     PDI 
Sbjct: 192 LEPIQGEGGVLPAELAYLQGARELCNEHNALLVFDEVQTGMGRTGHLFAYQHYGVIPDIL 251

Query: 249 LLGKSLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQN 308
              KSLGGG +PI+A+L  +D+   L  GTHG+T+GGNPLACAV+ A +DV+N   ++  
Sbjct: 252 TSAKSLGGG-FPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAGAVIDVINTPEVLAG 310

Query: 309 ALDLGDRLLKHLQQIESE--LIVEVRGRGLFIGIELNVA----AQDYCEQMINKGVLCKE 362
                D+    L+QI  +  L  +VRG GL IG  L+ A    A+D       +G++  +
Sbjct: 311 VNAKHDKFKARLEQIGEKYGLFTQVRGLGLLIGCVLSDAWKGKAKDIFNAAEQEGLMILQ 370

Query: 363 TQGNIIRIAPPLVIDKDEID 382
              +++R AP LV++  +ID
Sbjct: 371 AGPDVVRFAPSLVVEDADID 390


Lambda     K      H
   0.317    0.136    0.396 

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: 354
Number of extensions: 15
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: 394
Length of database: 406
Length adjustment: 31
Effective length of query: 363
Effective length of database: 375
Effective search space:   136125
Effective search space used:   136125
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 (21.6 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