GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Shewanella loihica PV-4

Align Acetylornithine aminotransferase 1; ACOAT 1; EC 2.6.1.11 (uncharacterized)
to candidate 5209240 Shew_1718 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)

Query= curated2:Q9AAL3
         (392 letters)



>FitnessBrowser__PV4:5209240
          Length = 446

 Score =  162 bits (410), Expect = 2e-44
 Identities = 128/398 (32%), Positives = 199/398 (50%), Gaps = 32/398 (8%)

Query: 15  IVRGEGCWLYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADILWHAS-NLYRLPAQ 73
           +V  EGC L   DGR  +D  +       G+G P +++A++ Q   L H        P+ 
Sbjct: 32  VVSAEGCELILDDGRRLIDGTSSWWACVHGYGHPYILEAMQKQLSTLSHVMFGGITHPSA 91

Query: 74  EALATKLTDATFAD--RVFFANSGAEAVEAAIKTARRWQGAKGRPERYRVLTFGNAFHGR 131
            A++ KL   T  +  +VF A+SG+ AVE A+K A ++   +G P + R+LT  + +HG 
Sbjct: 92  IAVSKKLLAMTSDNLTKVFLADSGSIAVEVAMKMALQYWQGRGAPSKQRILTVKHGYHGD 151

Query: 132 TLATISATD-----QMKVREGFTP-LYDAFDTTPFND---------IEGAARAITPQTAA 176
           T A +S  D          E  T  L+     TPF +         +E    A     AA
Sbjct: 152 TFAAMSVCDPEGGMHTMFGEAVTQQLFAPAPKTPFGETLIADDLEAMEALLNAHHQTIAA 211

Query: 177 ILVEPI-QGEGGLTPATPGFLAGLRALCDQHDLLLILDEVQTGIGRTGHLFAHELYGVRP 235
           +++EPI QG G +   +  +L GLRALCD++ +LLILDE+ TG GRTG LFA++  G+  
Sbjct: 212 VIIEPIMQGAGAMHFYSADYLKGLRALCDRYKVLLILDEIATGFGRTGKLFAYQHAGIEA 271

Query: 236 DIIAVAKGLGGGF-PIGACLATEDAASGMTPG-----SHGSTYGGNPLACAVASAVLDAV 289
           DI+ + K L GG+  + A L +++ A G++        HG T+ GNPLACA ASA LD +
Sbjct: 272 DILCLGKALTGGYISLAATLCSDEVALGISDSPSGVFMHGPTFMGNPLACAAASASLDLI 331

Query: 290 LAPGFLETVRERAALVDALLERLLRRHSDLFVRA-QGHGLMRGLQVRASARDVVAH--LR 346
               + E V   AA+   + + L    +   V+A +  G +  +++  S           
Sbjct: 332 NQHQWPEQV---AAIEQQMKQELATASAIEGVKAVRCLGAVGVIEMTRSVNTAALQQAFV 388

Query: 347 DFGVMTVAAGADVVRLLPPLTISELEIAEAEARLLRAA 384
           D GV  V   +  + ++PP TIS  +++     +L  A
Sbjct: 389 DRGVW-VRPFSSYIYIMPPYTISAQQLSRLTQAMLEVA 425


Lambda     K      H
   0.322    0.137    0.405 

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: 405
Number of extensions: 19
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: 392
Length of database: 446
Length adjustment: 32
Effective length of query: 360
Effective length of database: 414
Effective search space:   149040
Effective search space used:   149040
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 (21.9 bits)
S2: 50 (23.9 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