GapMind for Amino acid biosynthesis

 

Aligments for a candidate for proB in Synechococcus elongatus PCC 7942

Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate Synpcc7942_2265 Synpcc7942_2265 glutamate-5-semialdehyde dehydrogenase

Query= metacyc::AT2G39800-MONOMER
         (717 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_2265 Synpcc7942_2265
           glutamate-5-semialdehyde dehydrogenase
          Length = 431

 Score =  339 bits (869), Expect = 2e-97
 Identities = 188/420 (44%), Positives = 262/420 (62%), Gaps = 7/420 (1%)

Query: 299 AVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVAR 358
           A A R ++R+L   S  DR+++L  IA  LE     I A N+ D  +A   G+  ++ AR
Sbjct: 12  AQATRAAARQLAQWSGADRQRLLSAIATTLEQEAPRILAANQADCEAATTEGIAPALYAR 71

Query: 359 LVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDA 418
           L +   K+++  A VR LA + DP+G++    E+ +GL+L++ + P+GVL ++FE+RPDA
Sbjct: 72  LKLDADKLAAAIAGVRDLAQLPDPLGQIQIDRELDEGLILQRLTCPVGVLGVIFEARPDA 131

Query: 419 LVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPETVGG-KLIGLVTSREEIPDL 477
           ++QIASLAI+SGNG +LKGG+EA  S   +   I  A+ E     + I L+TSREE   L
Sbjct: 132 VIQIASLAIKSGNGAILKGGREAICSCQAIVAAIAQALAEQQAPVEAIRLLTSREETLAL 191

Query: 478 LKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKL 537
           LKLD  +DL+IPRGSN  V  +++ T IPVLGHADGICH+YVD+A   +    I  DAK 
Sbjct: 192 LKLDRYVDLIIPRGSNSFVRFVQDNTHIPVLGHADGICHLYVDQAAAIEKTVTITVDAKT 251

Query: 538 DYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEA--RSFNH 595
            YPAACNA+ETLL+H+ +     L  +  AL   GV+L G   A  I+ +  A    +  
Sbjct: 252 QYPAACNAIETLLIHEAIAPQ-FLPVVAAALHEKGVSLRGDAAAQTIVPMEAATEEDWRT 310

Query: 596 EYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTR 655
           EY      V +V  +  AI HI+ +GS HTD I TED   A  F  QVDSA V+HN STR
Sbjct: 311 EYSDLVLAVRLVPSLDAAIAHINEYGSGHTDAIATEDAAAAAQFFSQVDSAGVYHNCSTR 370

Query: 656 FSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQVV---DGDNGIVYTHQD 712
           F+DGFR+G GAEVG+ST ++  RGPVG+EGL+T ++++ G GQ+     G     + H+D
Sbjct: 371 FADGFRYGFGAEVGISTQKLPPRGPVGLEGLVTYKYVLSGDGQIAATYSGAQAKPFLHRD 430


Lambda     K      H
   0.318    0.135    0.378 

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: 593
Number of extensions: 20
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: 717
Length of database: 431
Length adjustment: 36
Effective length of query: 681
Effective length of database: 395
Effective search space:   268995
Effective search space used:   268995
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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