GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Sinorhizobium meliloti 1021

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate SMc02138 SMc02138 acetylornithine transaminase

Query= reanno::WCS417:GFF4238
         (406 letters)



>FitnessBrowser__Smeli:SMc02138
          Length = 399

 Score =  337 bits (863), Expect = 5e-97
 Identities = 176/376 (46%), Positives = 241/376 (64%), Gaps = 5/376 (1%)

Query: 30  RGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVSNVFTNEPALRL 89
           RGEG  +  + G   +DFA G+AVN LGHAHP LV AL  QA K+WH+SN++       L
Sbjct: 20  RGEGVWLIAEDGTRYLDFAAGVAVNSLGHAHPHLVEALKAQADKVWHLSNLYEIAGQESL 79

Query: 90  AHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALNSFHGRTLFTV 149
           A +L   TFA+RVFF NSGAEA E A K ARR  F +   EK+ +I    +FHGRTL T+
Sbjct: 80  ARRLTQVTFADRVFFTNSGAEALECAIKTARRYHFAKGHVEKFHVITFEGAFHGRTLATI 139

Query: 150 NVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVSDKTCAVVLEPIQGEGGVLPAELAYL 209
             GGQ KY +GFGPK  G   VP+ D+ A+K A++++T A+++EPIQGEGG+  A   ++
Sbjct: 140 AAGGQQKYIEGFGPKAPGFYQVPFGDIGAVKNAINEETAAILVEPIQGEGGIRTASKEFM 199

Query: 210 QGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVTPDILTSAKSLGGGFPIAAMLTT 269
           QG R+LCD    LL+ DEVQ+G+GR+G LFA++  G+ PDI+  AK +GGGFP+ A L T
Sbjct: 200 QGLRELCDEFGLLLILDEVQSGVGRTGKLFAHEWAGIKPDIMAVAKGIGGGFPLGACLAT 259

Query: 270 EALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLAGVNAKHDLFKARLEQIGKQY 329
           EA A  +V GTHG+TYGGNPLA AV  AV+DV+     L  V     +F+  L  +  ++
Sbjct: 260 EAAAAGMVAGTHGSTYGGNPLAMAVGNAVLDVVLAEGFLDQVREVALVFRQGLASLKDRF 319

Query: 330 -GIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKENLMILQAGPDVVRFAPSLVVEDAD 388
             +  E+RG GL+LG       K  + D+  A   E L+++ AG +V+R  P L+   A+
Sbjct: 320 PDVIEEIRGDGLMLGI----KAKVPSADLLKAIRAEKLLVVPAGENVLRLLPPLITTPAE 375

Query: 389 IKEGLDRFERAVKALT 404
            +EGL R ERA +A++
Sbjct: 376 AREGLARLERAAEAVS 391


Lambda     K      H
   0.320    0.137    0.400 

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: 444
Number of extensions: 15
Number of successful extensions: 2
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: 406
Length of database: 399
Length adjustment: 31
Effective length of query: 375
Effective length of database: 368
Effective search space:   138000
Effective search space used:   138000
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 (21.8 bits)
S2: 50 (23.9 bits)

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