GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Sinorhizobium fredii NGR234

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate WP_164924158.1 NGR_RS12135 aspartate aminotransferase family protein

Query= curated2:Q4A0N2
         (394 letters)



>NCBI__GCF_000018545.1:WP_164924158.1
          Length = 399

 Score =  249 bits (636), Expect = 1e-70
 Identities = 137/370 (37%), Positives = 209/370 (56%), Gaps = 8/370 (2%)

Query: 19  LKLALAKGRGAKVWDIEDNC--YIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSRAL 76
           L+  L   RG  VW I ++   Y+D  +G +V + GH HP +++AL+ Q++++  VS   
Sbjct: 12  LRAPLRFERGEGVWLIAEDGTRYLDFAAGVAVNSLGHAHPHLVEALKAQAEKLWHVSNLY 71

Query: 77  YSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAMNG 136
                     ++  +   + V   N+G EA+E AIK AR++             +I   G
Sbjct: 72  DVPGQESLARRLTAVTFADRVFFTNSGAEALECAIKTARRY--HFAKGHPERFHVITFEG 129

Query: 137 NFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQGEG 196
            FHGRT+ +++   Q  Y +GFGP     +   FGDI  +K  IN++T AI++EPIQGEG
Sbjct: 130 AFHGRTIATIAAGGQQKYIEGFGPKAPGFYQVPFGDIAAVKNAINDETAAILIEPIQGEG 189

Query: 197 GVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSLGG 256
           G+ +    F+QE+R LC+EY +LLI DE+Q G+GRTGK+FA EW    PDI  + K +GG
Sbjct: 190 GIRLASKEFMQELRALCDEYGLLLILDEVQCGVGRTGKLFAHEWSGITPDIMAVAKGIGG 249

Query: 257 GLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGDRL 316
           G +P+ A LA +   + +  GTHGST+GGNPLA AV  A LDV+  E  ++N  D+    
Sbjct: 250 G-FPLGACLATEAAAAGMVAGTHGSTYGGNPLAMAVGNAVLDVVLAEGFLENVRDVALVF 308

Query: 317 LKHLQQIES---ELIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIRIAPP 373
            + L  ++    ++I E+RG GL +GI+  V   D  + +  + +L      N++R+ PP
Sbjct: 309 RQGLASLKDRFPDVIEEIRGDGLMLGIKAKVPCADVLKAIRAEKLLAVPAGENVLRLLPP 368

Query: 374 LVIDKDEIDE 383
           L+    E  E
Sbjct: 369 LITTAAEARE 378


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: 13
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 394
Length of database: 399
Length adjustment: 31
Effective length of query: 363
Effective length of database: 368
Effective search space:   133584
Effective search space used:   133584
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 Apr 09 2024. 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