GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Herbaspirillum seropedicae SmR1

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate HSERO_RS22025 HSERO_RS22025 aromatic amino acid aminotransferase

Query= CharProtDB::CH_004054
         (397 letters)



>FitnessBrowser__HerbieS:HSERO_RS22025
          Length = 396

 Score =  454 bits (1169), Expect = e-132
 Identities = 220/397 (55%), Positives = 283/397 (71%), Gaps = 3/397 (0%)

Query: 1   MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60
           MF  +  YAGDPIL+LME+F+ D RS+KVNLSIG+Y +  G++P L +V  A A + AQ 
Sbjct: 1   MFSHLPPYAGDPILSLMEQFQRDERSNKVNLSIGIYTDGKGVVPVLPSVRTAAAAV-AQA 59

Query: 61  HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120
               +YLPMEG   YR A+A LLFGAD P    + +A +QTLGGSGALKVGAD + R+FP
Sbjct: 60  DAPYVYLPMEGHGAYRQAVAKLLFGADLPA--PEHLAIVQTLGGSGALKVGADLIARFFP 117

Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180
           +  +W+ DPTW+NH+ IF GAGF+   YP+YD  T G+ F  +LA + +LP  ++VLLHP
Sbjct: 118 QPTIWLPDPTWDNHIGIFEGAGFKTERYPYYDAQTKGLNFEGMLAKIDSLPRGAVVLLHP 177

Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240
           CCHNPTG D T  QW+ ++E+++ R L+PF D+AYQGF   ++ED + +R      +P  
Sbjct: 178 CCHNPTGVDPTRAQWEQIVEVVEKRGLLPFFDLAYQGFAESLDEDIWPVREAVRRQIPFF 237

Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300
           +SNSFSKIFSLY ER+G LSV C  A  A  VLGQLK TVRRNYSSPP  GA +VA VL 
Sbjct: 238 LSNSFSKIFSLYSERIGALSVFCPQAGQAANVLGQLKLTVRRNYSSPPRNGALLVAHVLG 297

Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360
           D+ L A W  EVEEMR R+  MR +L   L + +P+++F +LL Q GMF YTGLS+AQVD
Sbjct: 298 DDKLAAQWRGEVEEMRVRVRDMRVKLASQLKSAVPDQDFSFLLRQNGMFGYTGLSSAQVD 357

Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397
           RLREEFGVY + +GR+CVAGLN +NV RVA+  A V+
Sbjct: 358 RLREEFGVYAVGTGRICVAGLNDSNVARVAETMAEVL 394


Lambda     K      H
   0.320    0.135    0.401 

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: 446
Number of extensions: 10
Number of successful extensions: 3
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: 397
Length of database: 396
Length adjustment: 31
Effective length of query: 366
Effective length of database: 365
Effective search space:   133590
Effective search space used:   133590
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