GapMind for Amino acid biosynthesis

 

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

Align aspartate aminotransferase (EC 2.6.1.1) (characterized)
to candidate 5209481 Shew_1951 aromatic amino acid aminotransferase (RefSeq)

Query= metacyc::MONOMER-13012
         (397 letters)



>FitnessBrowser__PV4:5209481
          Length = 396

 Score =  483 bits (1243), Expect = e-141
 Identities = 230/395 (58%), Positives = 292/395 (73%), Gaps = 1/395 (0%)

Query: 1   MFSVLKPLPTDPILGLMAAYKQDTNPNKIDLGVGVYKDELGNTPVLKAVKKAEAFRLENE 60
           MF  L P+P DPILGLM  +++D + NK+DLGVGVYKDE GNTP+L  VK+AE  R++ E
Sbjct: 1   MFENLSPMPADPILGLMTKFREDPHANKVDLGVGVYKDEAGNTPILACVKRAEQHRIDTE 60

Query: 61  TSKSYIGLAGNLDYCQKMESLLLGE-HKTLLANRVRTAQAPGGTGALRVAAEFIMRCNPK 119
            +K YIG  G+  + Q M  L  G+ +  LLA+R+RT   PGGTGALRVAA+FI R NP 
Sbjct: 61  ATKVYIGPTGSPAFNQLMGELAFGQDNPALLADRIRTVSTPGGTGALRVAADFIKRVNPN 120

Query: 120 ATVWVTTPTWANHISLFEAAGLTVKEYPYYDYENKDLLFDEMINTLKQVPKGDVVLLHAC 179
           + +WV+ PTWANH  LFEAAG+ VK YPYYDY+NK L FDEM+  L Q+   DVVL HAC
Sbjct: 121 SVIWVSDPTWANHTGLFEAAGIKVKTYPYYDYQNKTLKFDEMLAALSQIGADDVVLFHAC 180

Query: 180 CHNPSGMDLNEAQWKVVAELAKEVGFTPLVDIAYQGFGSSLEEDARGLRILADAVEELII 239
           CHNPSGMDL   QW  V  L K+ GFTPL+D+AYQGFG  ++EDA G+R +A  V+++I+
Sbjct: 181 CHNPSGMDLTNEQWDQVIALTKQQGFTPLIDMAYQGFGDGVDEDAYGVRQMAANVDDMIL 240

Query: 240 CSSCSKNFGLYRERIGACSLIAKDSATADISNSVLLSVVRSIYSMPPAHGADIVNTILSS 299
           CSSCSKNFGLYRERIGACS++ KDS +A+++ SVLL VVR IYSMPPAHGA IV TIL S
Sbjct: 241 CSSCSKNFGLYRERIGACSIVGKDSHSANVAYSVLLYVVRCIYSMPPAHGAAIVETILGS 300

Query: 300 TELTQMWHQELDEMRSRINGLRTQIKETLATKDIAQDFSFIERQHGMFSFLGINKEQITR 359
           +EL Q W  EL  MR RING R  +   L  K + +DFSFI +Q GMFSFLG+  EQ+ +
Sbjct: 301 SELKQQWLDELKVMRDRINGNRAMLVNKLIEKGVTRDFSFIAKQKGMFSFLGVTPEQVAK 360

Query: 360 LQKEYGIYIVGSSRVNVAGVSDANIEYFANAVADV 394
           LQ ++ IY+V SSR+++AG+ + N++Y A ++A V
Sbjct: 361 LQADHSIYMVDSSRISIAGIGEGNVDYLAESIAKV 395


Lambda     K      H
   0.318    0.134    0.388 

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: 469
Number of extensions: 14
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: 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 ( 7.3 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