GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Streptacidiphilus oryzae TH49

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_037575899.1 BS73_RS24325 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::P9WPZ5
         (397 letters)



>NCBI__GCF_000744815.1:WP_037575899.1
          Length = 398

 Score =  394 bits (1013), Expect = e-114
 Identities = 214/388 (55%), Positives = 259/388 (66%), Gaps = 14/388 (3%)

Query: 6   LRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGV-NQYPPGPGSA 64
           L    TT+FAEMSALAT  GA+NLGQGFPD DGP  + +AA  A+  G  NQYPPGPG  
Sbjct: 21  LEGMGTTIFAEMSALATTTGAINLGQGFPDTDGPEAVREAAVRALREGRGNQYPPGPGVP 80

Query: 65  PLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSP 124
            LR A+A  + R +G+D+DP+TEVLVT GATEAIAA++L L+EPG EV+  EPFYDSY+ 
Sbjct: 81  ELRAAVAEHQLRFYGLDFDPDTEVLVTAGATEAIAASMLALLEPGDEVIAFEPFYDSYAA 140

Query: 125 VVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAI 184
            +AMAGA RV  P       F  D D LR  +TP TR L++NSPHNPTG VL   EL AI
Sbjct: 141 CIAMAGAKRV--PFTLRAPSFRPDLDELRALITPSTRLLLLNSPHNPTGMVLDDEELRAI 198

Query: 185 AEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWA 244
           A +AV  +L+V+TDEVYEHLVF+ A H P+A   GM ERT++ISSA K F+ TGWK+GW 
Sbjct: 199 AALAVEHDLLVVTDEVYEHLVFEGA-HRPIAALPGMRERTVSISSAGKTFSFTGWKVGWV 257

Query: 245 CGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTE 304
              A L+A VR AKQYL+YV   PFQ AVA AL   DA+    R SLR RRD L AGL  
Sbjct: 258 TAAAPLVAAVRTAKQYLTYVSAGPFQYAVAEALRLPDAYYEDFRASLRRRRDLLDAGLRA 317

Query: 305 IGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFC-DPAAGQASQQA 363
            GF V++  GTYF+  D  P G  D+  FC +LPE+ GV A+P S F  DP AG++    
Sbjct: 318 AGFEVYEPQGTYFITTDIAPFGAKDAYAFCRSLPERCGVVAVPNSVFYDDPEAGRSQ--- 374

Query: 364 DVWNHLVRFTFCKRDDTLDEAIRRLSVL 391
                 VRFTFCK+++ L EA  RL  L
Sbjct: 375 ------VRFTFCKKEEVLREAAARLQRL 396


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: 504
Number of extensions: 24
Number of successful extensions: 5
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: 398
Length adjustment: 31
Effective length of query: 366
Effective length of database: 367
Effective search space:   134322
Effective search space used:   134322
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 Jul 26 2024. The underlying query database was built on Jul 25 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