GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Herbaspirillum seropedicae SmR1

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate HSERO_RS15115 HSERO_RS15115 aminotransferase

Query= BRENDA::P9WPZ5
         (397 letters)



>FitnessBrowser__HerbieS:HSERO_RS15115
          Length = 385

 Score =  279 bits (714), Expect = 9e-80
 Identities = 156/389 (40%), Positives = 224/389 (57%), Gaps = 10/389 (2%)

Query: 3   VSRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPG 62
           V++L    TT+F  MSALA+  GAVNLGQGFPD    P ++ A   A+  G+NQYPP  G
Sbjct: 7   VTKLPKVGTTIFTVMSALASEKGAVNLGQGFPDFHCDPALVAAVTQAMQEGLNQYPPMAG 66

Query: 63  SAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSY 122
              LR AIA +  + +G  YDP +E+ VT GAT+ I  +VL  V PG EV++IEP YD Y
Sbjct: 67  VPVLREAIAEKVEKLYGHRYDPVSEITVTAGATQGILTSVLCAVHPGDEVIVIEPVYDCY 126

Query: 123 SPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELA 182
            P + +AG   V V +    +G+++  D ++ AVTP+TR +++N+PHNPTG+V+ A ++A
Sbjct: 127 VPAIELAGGVPVFVQMEVGAQGYSIPWDKVKAAVTPKTRMIMVNTPHNPTGSVMRAADVA 186

Query: 183 AIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIG 242
           A+A+I    ++++++DEVYEH+V+D   H  LA    +AER+   SS  K ++ TGWK+G
Sbjct: 187 ALADIVRGTDILILSDEVYEHMVYDGQPHESLARHPELAERSFINSSFGKTYHVTGWKVG 246

Query: 243 WACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGL 302
           +   PA L A  R   Q+  +    P Q  +A A   + A    L    + +RD    GL
Sbjct: 247 YVAAPAALTAEFRKVHQFNVFTVNTPVQYGLA-AYMKDPAPYLDLPAFYQHKRDLFRTGL 305

Query: 303 TEIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQ 362
               F +  S GTYF C     +      EFC  L  ++GVAAIP+SAF +         
Sbjct: 306 ANTRFELLPSQGTYFQCVKYGAISALPEAEFCKWLTSEIGVAAIPVSAFYNTPRESG--- 362

Query: 363 ADVWNHLVRFTFCKRDDTLDEAIRRLSVL 391
                 +VRF F K+D+TL  A+ RL+ L
Sbjct: 363 ------IVRFCFAKKDETLQLALERLAKL 385


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: 403
Number of extensions: 18
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: 385
Length adjustment: 31
Effective length of query: 366
Effective length of database: 354
Effective search space:   129564
Effective search space used:   129564
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 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