GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Shewanella oneidensis MR-1

Align phenylalanine aminotransferase (EC 2.6.1.57) (characterized)
to candidate 201550 SO2406 aspartate aminotransferase (NCBI ptt file)

Query= reanno::Marino:GFF879
         (395 letters)



>FitnessBrowser__MR1:201550
          Length = 396

 Score =  400 bits (1029), Expect = e-116
 Identities = 198/396 (50%), Positives = 267/396 (67%), Gaps = 3/396 (0%)

Query: 1   MFEALQPLPQDPILQLMQTFLEDDRPDKVDLGIGVYKDDAGNTPIMAAVHEAERRLLEGE 60
           MF +L  +P DPIL L+  + ED  P KVDLG+GVYKD AGNTPI+  V +AE+  LE E
Sbjct: 1   MFNSLIAMPADPILGLLTQYREDTHPQKVDLGVGVYKDPAGNTPILNCVKKAEKFRLETE 60

Query: 61  TTKSYVGPAGSAGFNSAMAELILGSNSPLVRDGRVSVIQTPGGCGALRMAAEFLRLCKAD 120
           TTK Y+GP GS  FN+ M EL  GS+   +   R+  + TPGG GALR+A +F++ C  +
Sbjct: 61  TTKVYIGPTGSPQFNTLMTELAFGSDHSAIIANRIRTVSTPGGTGALRVAGDFIKRCNPN 120

Query: 121 TKVWVSTPTWANHLPLLGGAGLTIREYPYLNPETLQVDFGAMLETLERADAGDVVLLHGC 180
             +WVS PTWANH  L   AG+T++ YPY + ++  + F  ML  L +    DVVLLH C
Sbjct: 121 AVLWVSDPTWANHTGLFEAAGITVKTYPYYDYDSKSLKFDEMLAALSQVSPDDVVLLHAC 180

Query: 181 CHNPSGADLSLAQWQEVTSLIQRKGLLPFVDMAYQGLGEGLDADAAGLRHLASAVPEMLI 240
           CHNPSG DL+  QW +V +L + +G  P +DMAYQG G+G+D DA G+R +A+AV  M++
Sbjct: 181 CHNPSGMDLTTDQWDKVVTLTKEQGFTPLIDMAYQGFGDGVDIDAYGVRKMAAAVDNMIL 240

Query: 241 AASCSKNFGLYRERTGALALVSETATVNAAATSQLLSVIRSHYSMPPAHGASIVETILGD 300
            +SCSKNFGLYRER G+ ++V++ A     A S LL V+R  YSMPPAHGA+IVETILG 
Sbjct: 241 CSSCSKNFGLYRERIGSCSVVAKDANTANIAQSVLLYVVRCLYSMPPAHGAAIVETILGS 300

Query: 301 DDLRAQWQQELNGMCKRILHLRHAFADALSPVG---DFDFIARQRGMFSFLGISPEQVGR 357
            +L  +W  EL  M  RI   R    + L   G   DF FIARQ+GMFSFLG++PEQV R
Sbjct: 301 KELTQEWLDELKVMRDRINGNRAILVEKLKANGVARDFSFIARQKGMFSFLGVNPEQVAR 360

Query: 358 LRKEHGIHMLESSRVNVAGLNDHVLPQVASALREVL 393
           L+KE  I+M+ SSR+++AG+++  +  +A ++ +VL
Sbjct: 361 LQKEFSIYMVGSSRISIAGISEDNVDYLAQSIAKVL 396


Lambda     K      H
   0.320    0.136    0.402 

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: 384
Number of extensions: 8
Number of successful extensions: 2
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: 395
Length of database: 396
Length adjustment: 31
Effective length of query: 364
Effective length of database: 365
Effective search space:   132860
Effective search space used:   132860
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: 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