GapMind for Amino acid biosynthesis

 

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

Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 7023699 Shewana3_0929 GntR family transcriptional regulator (RefSeq)

Query= reanno::azobra:AZOBR_RS06555
         (404 letters)



>FitnessBrowser__ANA3:7023699
          Length = 470

 Score =  159 bits (401), Expect = 2e-43
 Identities = 117/384 (30%), Positives = 194/384 (50%), Gaps = 21/384 (5%)

Query: 24  LLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEGFTPLREW 83
           +L+  ++  I+ F    PDP  FP  A+AR+  K+ +  S +  A    +  G   LR+ 
Sbjct: 97  VLQASKQAGIVPFGSAFPDPSLFPQQALARSLVKVTRQMSPSFAA--DNLPPGNAGLRKA 154

Query: 84  ICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQAFSPYEP 143
           I     + G+    DE+L+TSG+ +AL      L   G+ +++  PT+ GA+QA    + 
Sbjct: 155 ISQRYAKLGMSVAPDEILITSGAMEALNLSLAALAQAGDWVVIESPTFYGAMQAIERLKL 214

Query: 144 QYLSVPGD-AEGPDLAAVEAALEQKP-KFFYLVPDFQNPNGTTISLARREALLDLCAKHG 201
           + ++V  D  EG DL A+   L+  P K  +L+   QNP G ++S  +++A+  L  +H 
Sbjct: 215 RAIAVATDPREGIDLNALAEVLKTYPVKACWLMSLHQNPLGCSLSDQKKQAVYQLLCEHN 274

Query: 202 VPIVEDAAYTELRYEGEPIPSMV-ALDAARNGGKITNVLFCGSFSKTMVPALRVGWI--N 258
           V ++ED  Y EL Y G   P  + ALD          VL CGSFSK+++   RVGW+   
Sbjct: 275 VSLIEDDVYQEL-YVGSSAPRPIKALDTQ------GCVLHCGSFSKSLIAGYRVGWVAAG 327

Query: 259 GPAEVINRLVLMKQAGDLHTSTINQIVLHDVV-SQNFDSHIRRLRAGYKERRDAMLTALS 317
             A  + RL LM     L TS   Q+ + D + S  ++ H++RLR    +R+ AM   L 
Sbjct: 328 RHAPQLQRLQLM---STLSTSAPMQLAIADFIQSPQYERHLKRLRHTLADRKFAMYQLLR 384

Query: 318 EFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGKNTLR 377
              P  V+     GG F+W+ LP   D   +   A+ +  ++  PG+ F      ++ +R
Sbjct: 385 AHLPESVSVNFEPGGYFLWLALPSHMDATQIYHSAL-ERGISIAPGNLFSNQAEFRHFMR 443

Query: 378 LSFSNN-NPERIREGIRRLCGLLQ 400
           ++ S + +PE +R  ++ L  +L+
Sbjct: 444 INASYDCSPELVR-AVKALAQILE 466


Lambda     K      H
   0.320    0.138    0.410 

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: 424
Number of extensions: 18
Number of successful extensions: 5
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: 470
Length adjustment: 32
Effective length of query: 372
Effective length of database: 438
Effective search space:   162936
Effective search space used:   162936
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: 51 (24.3 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