GapMind for Amino acid biosynthesis

 

Aligments for a candidate for proB in Shewanella loihica PV-4

Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate 5210406 Shew_2847 gamma-glutamyl phosphate reductase (RefSeq)

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



>lcl|FitnessBrowser__PV4:5210406 Shew_2847 gamma-glutamyl phosphate
           reductase (RefSeq)
          Length = 429

 Score =  259 bits (663), Expect = 1e-73
 Identities = 148/401 (36%), Positives = 235/401 (58%), Gaps = 11/401 (2%)

Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361
           A+ +S  + +L++  ++ +L  IA  L      I A N+ DVA A+E GL ++M+ RL++
Sbjct: 21  AKAASYAMASLTASQKRDLLRAIAAKLTDKRAQIVAANQQDVAKARENGLNDAMIDRLLL 80

Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421
              ++S + A +  +  + DPIG  L+   + +GL L +   PLGVL +++E+RP+  V 
Sbjct: 81  DESRLSGVIADIENVVALADPIGSELESQLLDNGLRLSRRRVPLGVLGVIYEARPNVTVD 140

Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEIPDLL 478
           IA LA+++GN ++L+GGKE   SN  L + I +AI E  +    + L+    R  +  LL
Sbjct: 141 IAVLALKTGNAVILRGGKETLASNLALSEAIREAISEQGLPSDAVQLIQDPDRALVSGLL 200

Query: 479 KLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKLD 538
           KLD  +D+++PRG   L         IPV+    GICH+YVD   D   A  ++++AK+ 
Sbjct: 201 KLDKYVDMIVPRGGQNLQRLCAEQATIPVILGGIGICHLYVDSEVDQLKAIEVIANAKVQ 260

Query: 539 YPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYG-------GPRASKILNIPEAR 591
            P  CNA++T+LVH+ + Q   L +L   L + GV+ +        G  A  + +     
Sbjct: 261 RPTVCNALDTVLVHQSIAQ-TFLPKLYAHLSALGVSFHACDQAEAIGKDAGTVTHQASDE 319

Query: 592 SFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHN 651
           +F  E+ +    V VV+D+  AI HI R  S H++ I++++      F+ +VD+AAV+ N
Sbjct: 320 TFGTEWLSLNLGVRVVDDMDMAIAHIRRFSSGHSEGILSDNIHATARFINEVDAAAVYVN 379

Query: 652 ASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWI 692
           ASTRF+DG +FGLGAEV VST ++HARGP+G+E L T +WI
Sbjct: 380 ASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWI 420


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: 579
Number of extensions: 28
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: 429
Length adjustment: 36
Effective length of query: 681
Effective length of database: 393
Effective search space:   267633
Effective search space used:   267633
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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