GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Shewanella sp. ANA-3

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate 7025921 Shewana3_3070 aspartate carbamoyltransferase (RefSeq)

Query= BRENDA::Q51742
         (315 letters)



>FitnessBrowser__ANA3:7025921
          Length = 339

 Score =  114 bits (286), Expect = 3e-30
 Identities = 100/320 (31%), Positives = 151/320 (47%), Gaps = 22/320 (6%)

Query: 7   GRDLLCLQDYTAEEIWTILETAKMFKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEV 66
           G  +L +     + I TI   A     +    K  ++LEG  L  +F +PSTRTRVSF  
Sbjct: 6   GSHILSVNQLDLDSIQTIFNVAHRMMPYALREKRTKVLEGAILGNLFFEPSTRTRVSFGC 65

Query: 67  AMAHLGGHALYLNAQ-DLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYATVP 125
           A   LGGH           L +GE++ DTARVLS Y D I  R  D   V++ A+ + VP
Sbjct: 66  AFNLLGGHVRETTGMASSSLSKGESLYDTARVLSTYSDVIAMRHPDSYSVKEFAEGSRVP 125

Query: 126 VINGLSDFS--HPCQALADYMTIWEKKG----TIKGVKVVYVGD--GNNVAHSL--MIAG 175
           VING  D S  HP QAL D  TI ++ G     I G+ +  VGD       HSL  ++  
Sbjct: 126 VING-GDGSNEHPTQALLDLFTIQKELGHAGRGIDGMHIAMVGDLKFGRTVHSLSRLLCM 184

Query: 176 TKLGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASM 235
            K  +  +++  E   PD     +   +   +G S ++       +  AD++Y       
Sbjct: 185 YKNISFTLISPTELAMPD-----YVISDIENAGHSIKITDQLEGHLDKADILYL-TRIQE 238

Query: 236 GQEAEAEERRKIFRPFQVNKDL-VKHAKPDYMFMHCLPAH---RGEEVTDDVIDSPNSVV 291
            +    EE  K    F++N+ +  +H K + + MH LP     +  E+ +D+   PN  +
Sbjct: 239 ERFPSQEEANKYRGKFRLNRSIYTQHCKSNTVIMHPLPRDSRAQANELDNDLNSHPNLAI 298

Query: 292 WDQAENRLHAQKAVLALVMG 311
           + QA+N L  + A+ AL +G
Sbjct: 299 FRQADNGLLIRMALFALTLG 318


Lambda     K      H
   0.319    0.134    0.400 

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: 230
Number of extensions: 14
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: 315
Length of database: 339
Length adjustment: 28
Effective length of query: 287
Effective length of database: 311
Effective search space:    89257
Effective search space used:    89257
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: 48 (23.1 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