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 5209481 Shew_1951 aromatic amino acid aminotransferase (RefSeq)

Query= BRENDA::A0A140ND68
         (396 letters)



>FitnessBrowser__PV4:5209481
          Length = 396

 Score =  404 bits (1038), Expect = e-117
 Identities = 198/396 (50%), Positives = 266/396 (67%)

Query: 1   MFENITAAPADPILGLADLFRADERPGKINLGIGVYKDETGKTPVLTSVKKAEQYLLENE 60
           MFEN++  PADPILGL   FR D    K++LG+GVYKDE G TP+L  VK+AEQ+ ++ E
Sbjct: 1   MFENLSPMPADPILGLMTKFREDPHANKVDLGVGVYKDEAGNTPILACVKRAEQHRIDTE 60

Query: 61  TTKNYLGIDGIPEFGRCTQELLFGKGSALINDKRARTAQTPGGTGALRVAADFLAKNTSV 120
            TK Y+G  G P F +   EL FG+ +  +   R RT  TPGGTGALRVAADF+ +    
Sbjct: 61  ATKVYIGPTGSPAFNQLMGELAFGQDNPALLADRIRTVSTPGGTGALRVAADFIKRVNPN 120

Query: 121 KRVWVSNPSWPNHKSVFNSAGLEVREYAYYDAENHTLDFDALINSLNEAQAGDVVLFHGC 180
             +WVS+P+W NH  +F +AG++V+ Y YYD +N TL FD ++ +L++  A DVVLFH C
Sbjct: 121 SVIWVSDPTWANHTGLFEAAGIKVKTYPYYDYQNKTLKFDEMLAALSQIGADDVVLFHAC 180

Query: 181 CHNPTGIDPTLEQWQTLAQLSVEKGWLPLFDFAYQGFARGLEEDAEGLRAFAAMHKELIV 240
           CHNP+G+D T EQW  +  L+ ++G+ PL D AYQGF  G++EDA G+R  AA   ++I+
Sbjct: 181 CHNPSGMDLTNEQWDQVIALTKQQGFTPLIDMAYQGFGDGVDEDAYGVRQMAANVDDMIL 240

Query: 241 ASSYSKNFGLYNERVGACTLVAADSETVDRAFSQMKAAIRANYSNPPAHGASVVATILSN 300
            SS SKNFGLY ER+GAC++V  DS + + A+S +   +R  YS PPAHGA++V TIL +
Sbjct: 241 CSSCSKNFGLYRERIGACSIVGKDSHSANVAYSVLLYVVRCIYSMPPAHGAAIVETILGS 300

Query: 301 DALRAIWEQELTDMRQRIQRMRQLFVNTLQEKGANRDFSFIIKQNGMFSFSGLTKEQVLR 360
             L+  W  EL  MR RI   R + VN L EKG  RDFSFI KQ GMFSF G+T EQV +
Sbjct: 301 SELKQQWLDELKVMRDRINGNRAMLVNKLIEKGVTRDFSFIAKQKGMFSFLGVTPEQVAK 360

Query: 361 LREEFGVYAVASGRVNVAGMTPDNMAPLCEAIVAVL 396
           L+ +  +Y V S R+++AG+   N+  L E+I  VL
Sbjct: 361 LQADHSIYMVDSSRISIAGIGEGNVDYLAESIAKVL 396


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: 417
Number of extensions: 12
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: 396
Length adjustment: 31
Effective length of query: 365
Effective length of database: 365
Effective search space:   133225
Effective search space used:   133225
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