GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Sinorhizobium meliloti 1021

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate SMc04323 SMc04323 aminotransferase

Query= SwissProt::H3ZPL1
         (417 letters)



>FitnessBrowser__Smeli:SMc04323
          Length = 408

 Score =  317 bits (813), Expect = 3e-91
 Identities = 183/409 (44%), Positives = 246/409 (60%), Gaps = 15/409 (3%)

Query: 16  LDYEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLE-K 74
           LD+E  F+ ++  MKASEIRELLKL++  D+IS AGG+P PE FP +   E   E+    
Sbjct: 2   LDWESIFATRSSRMKASEIRELLKLLDRPDIISFAGGIPDPELFPNDAFREAYAEIFGGP 61

Query: 75  HAAQALQYGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGD 134
               ALQY  ++G+ PLR  LA  M     IP S  +I  TSGSQQ LD +G++F++P D
Sbjct: 62  SVGAALQYSISEGYRPLREWLAGQMAA-LGIPASVDNIFITSGSQQGLDYLGKLFLSPKD 120

Query: 135 IIVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPT 194
             +V  PTYL ALQAF  YEP + Q  L+  G          Q   + G +VK  Y    
Sbjct: 121 TALVTWPTYLGALQAFNAYEPSYDQ--LNPAGNRTPAAYA--QAAAEAGGRVKFAYLSAD 176

Query: 195 FQNPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWD-------EE 247
           F NP G T+    R+R+LELA + D  I+ED  Y  LRY GE + PI A +         
Sbjct: 177 FANPTGETVGRAGRERVLELAEELDIAIIEDAAYQSLRYDGEAIPPILALEIARKGDINS 236

Query: 248 GRVIYLGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYL 307
            R IY G+FSK LAPG R+GWI A    IRKL + KQ+ DL ++T +Q+      E G+ 
Sbjct: 237 TRTIYCGSFSKTLAPGLRVGWICAAEPVIRKLVLMKQAADLHSSTINQMAIATVAERGF- 295

Query: 308 DKHIPKIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVA 367
           ++ + KI + Y+ RRDAML ALE++MP GV WTKPEGGMF+W TLP+G D   +L K++ 
Sbjct: 296 EEQVAKIHKAYRQRRDAMLSALEKYMPAGVTWTKPEGGMFIWVTLPKGSDGAELLAKSIQ 355

Query: 368 KG-VAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEM 415
              VA+VPG AFFA    +NT+RL+F+   +  I EGI+RL + ++ E+
Sbjct: 356 TAKVAFVPGRAFFADGSGENTLRLSFSCANDRMIDEGIRRLGDLVRGEV 404


Lambda     K      H
   0.318    0.137    0.398 

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: 439
Number of extensions: 24
Number of successful extensions: 7
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: 417
Length of database: 408
Length adjustment: 31
Effective length of query: 386
Effective length of database: 377
Effective search space:   145522
Effective search space used:   145522
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 (21.7 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