GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Synechococcus elongatus PCC 7942

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase

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



>FitnessBrowser__SynE:Synpcc7942_0943
          Length = 422

 Score =  323 bits (829), Expect = 4e-93
 Identities = 182/405 (44%), Positives = 239/405 (59%), Gaps = 8/405 (1%)

Query: 6   APVQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVG 65
           +P     FD  ++  Y        RGEG RVWD  GR  +DF  GIA   LGHAHP LV 
Sbjct: 16  SPFSTDAFDACVMQTYGRFPLALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVD 75

Query: 66  ALTEQAHKLWHVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFD 125
           A+++Q  KL HVSN++      +LA  L   + A+RVFFCNSGAEANEAA KLAR+    
Sbjct: 76  AISDQIRKLHHVSNLYYIPEQGQLAAWLTANSCADRVFFCNSGAEANEAAIKLARKHGNT 135

Query: 126 RFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKA---- 181
              +E   I+ A  SFHGRTL  V   GQ KY  GF P + G  +VPYNDL AL+A    
Sbjct: 136 VLEAENPIILTAQASFHGRTLAAVTATGQPKYHKGFQPLVQGFRYVPYNDLAALEATLAE 195

Query: 182 --AVSDKTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLF 239
             A  +   A++LEP+QGEGGV P + AY Q  R LCD    LL+ DEVQ GMGRSG L+
Sbjct: 196 LDAAGETVAAILLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLLILDEVQVGMGRSGQLW 255

Query: 240 AYQHYGVTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVI 299
            Y++ G+ PD  T AK LGGG PI A+L  +A    L  G H +T+GGNPLAC    A+ 
Sbjct: 256 GYENLGIEPDAFTVAKGLGGGVPIGALL-VKASCNILQAGEHASTFGGNPLACRAGLAIA 314

Query: 300 DVINTPEVLAGVNAKHDLFKARLEQIGKQY-GIFTEVRGMGLLLGCVLSDAFKGKAKDVF 358
            V+   ++LA V A+ +  +A L+++  +Y  +   VRG GL+ G VL +        + 
Sbjct: 315 QVMERDQLLANVQARGEQLRAGLQELVDRYPNLLAGVRGWGLINGLVLRNDPNVTPIALV 374

Query: 359 NAAEKENLMILQAGPDVVRFAPSLVVEDADIKEGLDRFERAVKAL 403
            AA ++ L+++ AG +VVRF P L+V  A+I E L   ERA+ A+
Sbjct: 375 KAAIEQGLLLVPAGAEVVRFVPPLIVSAAEIDEALAMTERALLAI 419


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: 443
Number of extensions: 20
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: 406
Length of database: 422
Length adjustment: 31
Effective length of query: 375
Effective length of database: 391
Effective search space:   146625
Effective search space used:   146625
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.

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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