GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pseudomonas stutzeri RCH2

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate GFF1235 Psest_1268 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::P9WPZ5
         (397 letters)



>FitnessBrowser__psRCH2:GFF1235
          Length = 382

 Score =  249 bits (635), Expect = 1e-70
 Identities = 149/393 (37%), Positives = 210/393 (53%), Gaps = 13/393 (3%)

Query: 1   MTVSRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPG 60
           M +S+L    TT+F  MS LA   GA+NL QGFPD DGP  + +A    +  G NQY P 
Sbjct: 1   MLISKLPNVGTTIFTTMSQLAADTGALNLSQGFPDFDGPEALREAVAGHVMAGHNQYAPM 60

Query: 61  PGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYD 120
            G   LR  +AA+    +G D D   EV +T GAT+AI  A+  ++ PG EV++ +P YD
Sbjct: 61  TGLPALREQVAAKVAGLYGRDVDAAAEVTITPGATQAIFCAIQAVIRPGDEVIVFDPCYD 120

Query: 121 SYSPVVAMAGAHRVTVPL-VPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSAT 179
           SY P V +AG   +   L +PD   F +D   L  A+TPRTR +++N+PHNP+GA++ A 
Sbjct: 121 SYEPSVQLAGGVCIHQQLSLPD---FRIDWQRLADAITPRTRMIVLNTPHNPSGALIDAD 177

Query: 180 ELAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGW 239
           +L  +A +    ++ +++DEVYEHLVFD   H  +   D + +R   ISS  K ++ TGW
Sbjct: 178 DLDRLAALIRERDIYLLSDEVYEHLVFDGREHASVLRHDELYQRAFVISSFGKTYHVTGW 237

Query: 240 KIGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLA 299
           K G+   P  L   +R   QY+S+ G  P Q A+A  +      +A L    +A+RD   
Sbjct: 238 KTGYVVAPPMLSVELRKVHQYVSFTGVTPLQWALADFMAAHPEHLAELPAFYQAKRDLFC 297

Query: 300 AGLTEIGFAVHDSYGTYFLCADPRPLGYD-DSTEFCAALPEKVGVAAIPMSAFCDPAAGQ 358
             L    F+   + GTYF  AD   +  D D       L  + GVA IP+S F       
Sbjct: 298 DLLAGSRFSFTRAAGTYFQLADYSAIRPDLDDVAMAEWLTREHGVACIPISVF------- 350

Query: 359 ASQQADVWNHLVRFTFCKRDDTLDEAIRRLSVL 391
             Q       LVRF F KR++TL +A  RL  +
Sbjct: 351 -YQHPPANLRLVRFCFAKREETLRQAAERLCAI 382


Lambda     K      H
   0.321    0.135    0.405 

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: 398
Number of extensions: 11
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: 382
Length adjustment: 30
Effective length of query: 367
Effective length of database: 352
Effective search space:   129184
Effective search space used:   129184
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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