GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Marinobacter adhaerens HP15

Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate GFF1185 HP15_1162 aminotransferase, class I and II

Query= BRENDA::Q82IK5
         (364 letters)



>FitnessBrowser__Marino:GFF1185
          Length = 400

 Score =  159 bits (401), Expect = 2e-43
 Identities = 125/388 (32%), Positives = 183/388 (47%), Gaps = 32/388 (8%)

Query: 6   DRLPTFPWDKLEPYKARAAAHPDGI--VDLSVGTPVDPVPELIQKALVAAADS-PGYPTV 62
           DRL  +P++KL   KA  +  PD +  + L +G P  P P+ +++ +    D    YPT 
Sbjct: 6   DRLHPYPFEKLAKLKAGISV-PDHLRPISLGIGEPKHPSPDFVKQVIANNLDKLANYPTT 64

Query: 63  WGTPELRDALTGWVERRLGARGVT---HHHVLPIVGSKELV-AWLPTQLGLGPGDKVAHP 118
            GT ELR+A++GW  RR   +  +    ++++P+ G++E + + +   +       V  P
Sbjct: 65  RGTDELREAISGWATRRFNLKAGSLSAANNIVPVNGTREAIFSLVQAVVDATKPATVVSP 124

Query: 119 RLAYPTYEVGARLARADHVV------------YDDPTELDPTGLKLLWLNSPSNPTGKVL 166
              Y  YE  A LA A  V             +D   E      ++L+L SP NP+G V+
Sbjct: 125 NPFYQVYEGAAFLAGATPVYIPCDGSNGFIPDFDSVPESIWQECQILFLCSPGNPSGAVI 184

Query: 167 SKAELTRIVAWAREHGILVFSDECYLELGWEAD--PVSVLHPDVCGG--SYEGIVSVHSL 222
           S+  LTR++A A +H  +V SDECY EL  E    P  +L      G   Y   V  HSL
Sbjct: 185 SREALTRVIALADKHDFIVASDECYSELYPEEGNAPEGLLQTCAAIGRDDYARCVVFHSL 244

Query: 223 SKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQRERY 282
           SKRSNL G R+ F+AGD  +L   L+ R + G       Q A +AA  D+ HVRE R  Y
Sbjct: 245 SKRSNLPGLRSGFVAGDANILDGYLKYRTYHGCAMPIHNQLASIAAWSDEDHVRENRAAY 304

Query: 283 AARRTALRDALLSHGFRIEHSEASLYLWATRGESCWDTVAHL-ADLGILVAPGDFYG--- 338
            A+  A+   +L     ++  +A  YLW             L A   + V PG +     
Sbjct: 305 RAKFEAV-VPILREVMDVDFPDAGFYLWPITPMDDETFARELSAQQNVHVLPGRYLSRTV 363

Query: 339 ---SAGEQFVRVALTATDERVAAAVRRL 363
              + GE  VR+AL A  E    A  R+
Sbjct: 364 DGHNPGENRVRMALVAPLEECVEAAERI 391


Lambda     K      H
   0.319    0.135    0.420 

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: 419
Number of extensions: 24
Number of successful extensions: 4
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: 364
Length of database: 400
Length adjustment: 30
Effective length of query: 334
Effective length of database: 370
Effective search space:   123580
Effective search space used:   123580
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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