GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Sphingomonas indica Dd16

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_085217296.1 B9N75_RS02070 aminotransferase

Query= BRENDA::P9WPZ5
         (397 letters)



>NCBI__GCF_900177405.1:WP_085217296.1
          Length = 384

 Score =  297 bits (760), Expect = 4e-85
 Identities = 160/384 (41%), Positives = 230/384 (59%), Gaps = 13/384 (3%)

Query: 7   RPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPL 66
           R   T+VF  MS  A  +GAVNLGQGFPD   P  ++  A + + G  +QYPP  G   L
Sbjct: 6   RDIPTSVFERMSLAARELGAVNLGQGFPDFGWPEDVVAKAAELLTGAASQYPPMRGLPEL 65

Query: 67  RRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVV 126
           R A+A    +H G+ Y P+ E+ VT GATEA+A+A+L L+EPG EVLL +P YD+Y P+V
Sbjct: 66  RAAVADHYSQHQGIAYAPD-EITVTSGATEALASALLALIEPGDEVLLFQPLYDAYVPMV 124

Query: 127 AMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAE 186
              G     V L P    + +  +A+  A+TPRTR ++ N+PHNPTG   S  EL A+AE
Sbjct: 125 RRGGGVPRYVALRPPE--WRITREAIEAALTPRTRLVVFNNPHNPTGRAFSQDELTALAE 182

Query: 187 IAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACG 246
           + VA +L+V++DEV+EH++   A HLPLA   GM++RT+ + SA K+F+ TGWK+GW   
Sbjct: 183 VCVARDLIVLSDEVWEHVMPGGAAHLPLASLPGMSDRTVKVGSAGKIFSLTGWKVGWIAA 242

Query: 247 PAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEIG 306
           PA L   +  A Q++++      Q AVA  L  ++A+   +R +    RDRLA GL + G
Sbjct: 243 PAALGDPITKAHQFVTFTTPPNLQAAVAYGLGKDEAYYRDMRAAFAVARDRLADGLADAG 302

Query: 307 FAVHDSYGTYFLCADPRPLGY-DDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQADV 365
           + V    G+YFLC D    G   D   FC     + G+AAIP++AF         ++  V
Sbjct: 303 YVVLPGEGSYFLCVDLTASGIAADDLTFCERAVREAGIAAIPLTAF--------FEETPV 354

Query: 366 WNHLVRFTFCKRDDTLDEAIRRLS 389
            N ++R  F K+ +T+DE ++RL+
Sbjct: 355 TN-VIRLCFAKKQETIDEGLKRLA 377


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: 411
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: 384
Length adjustment: 31
Effective length of query: 366
Effective length of database: 353
Effective search space:   129198
Effective search space used:   129198
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.

Links

Downloads

Related tools

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