GapMind for Amino acid biosynthesis

 

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

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate 5209529 Shew_1999 aromatic amino acid aminotransferase (RefSeq)

Query= BRENDA::A0A140ND68
         (396 letters)



>FitnessBrowser__PV4:5209529
          Length = 397

 Score =  518 bits (1335), Expect = e-152
 Identities = 246/396 (62%), Positives = 312/396 (78%)

Query: 1   MFENITAAPADPILGLADLFRADERPGKINLGIGVYKDETGKTPVLTSVKKAEQYLLENE 60
           +F  +  APADPILGL D F+AD R  K+NLG+G+YKDE+G+TP+L SVK AEQ LLE E
Sbjct: 2   IFNQVVLAPADPILGLTDAFKADPRADKVNLGVGIYKDESGQTPILKSVKLAEQKLLETE 61

Query: 61  TTKNYLGIDGIPEFGRCTQELLFGKGSALINDKRARTAQTPGGTGALRVAADFLAKNTSV 120
           T+K+YLGIDG+  + +  Q LLFG   A++++KRA TAQ PGGTG+LR+AA+F+ +NT+ 
Sbjct: 62  TSKSYLGIDGVIAYNQAVQGLLFGTDHAVMSEKRAVTAQAPGGTGSLRMAAEFVVRNTAS 121

Query: 121 KRVWVSNPSWPNHKSVFNSAGLEVREYAYYDAENHTLDFDALINSLNEAQAGDVVLFHGC 180
           + VWVSN +W NH ++F SAGL V++Y YYDA +H +DFDA++ SL +A +GD++L HGC
Sbjct: 122 RTVWVSNLTWANHNNIFQSAGLTVKQYGYYDAASHDIDFDAMLTSLEQANSGDLLLLHGC 181

Query: 181 CHNPTGIDPTLEQWQTLAQLSVEKGWLPLFDFAYQGFARGLEEDAEGLRAFAAMHKELIV 240
           CHNPTGID  + QW+ +AQL V+KG +PLFDFAYQGF  G+EEDA+GLR  A+   EL+V
Sbjct: 182 CHNPTGIDLNICQWEVIAQLCVDKGLIPLFDFAYQGFGAGVEEDAQGLRLVASKVPELLV 241

Query: 241 ASSYSKNFGLYNERVGACTLVAADSETVDRAFSQMKAAIRANYSNPPAHGASVVATILSN 300
           A+S+SKNFGLYNER+GA TLVA D ET  RAFSQ+K+ IR++YSNPPAHGA +VATIL +
Sbjct: 242 ANSFSKNFGLYNERIGAVTLVAEDEETAKRAFSQIKSTIRSSYSNPPAHGALIVATILGD 301

Query: 301 DALRAIWEQELTDMRQRIQRMRQLFVNTLQEKGANRDFSFIIKQNGMFSFSGLTKEQVLR 360
             LR +WE+ELT MR+RI  MR LFV TL E+G  +DFSFI  QNGMFSFSGL K+QV R
Sbjct: 302 AELRKLWEEELTQMRERIAEMRVLFVKTLSEQGVEQDFSFISAQNGMFSFSGLNKDQVAR 361

Query: 361 LREEFGVYAVASGRVNVAGMTPDNMAPLCEAIVAVL 396
           L+EEFGVY V SGR++VAGMT  NM  +C AI  VL
Sbjct: 362 LKEEFGVYIVGSGRISVAGMTRANMDTICRAIAQVL 397


Lambda     K      H
   0.318    0.134    0.392 

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: 480
Number of extensions: 10
Number of successful extensions: 1
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: 396
Length of database: 397
Length adjustment: 31
Effective length of query: 365
Effective length of database: 366
Effective search space:   133590
Effective search space used:   133590
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