GapMind for Amino acid biosynthesis

 

Aligments for a candidate for proB in Shewanella sp. ANA-3

Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate 7023725 Shewana3_0955 gamma-glutamyl phosphate reductase (RefSeq)

Query= SwissProt::O04226
         (716 letters)



>lcl|FitnessBrowser__ANA3:7023725 Shewana3_0955 gamma-glutamyl
           phosphate reductase (RefSeq)
          Length = 425

 Score =  258 bits (660), Expect = 3e-73
 Identities = 145/409 (35%), Positives = 233/409 (56%), Gaps = 9/409 (2%)

Query: 296 REMAVAARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPL 355
           +++   A+  S  L NLS+ ++  +L  +A+AL  N   I + N  DVAAA+  G    +
Sbjct: 11  QQLGSQAKQASYALANLSAVQKADLLEAIAEALTQNTQAILAANAKDVAAAKAEGLNDAM 70

Query: 356 VARLTIKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESR 415
           + RL +   ++A +   I  +  + DP+ +      + + L L +   PLGV+ +++E+R
Sbjct: 71  IDRLLLNESRLAGIIGDIGDVVRLADPVGEEFGSRVLDNGLRLTRRRVPLGVIGVIYEAR 130

Query: 416 PDALVQIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIP-RNVGEKLIGLVTTRDE- 473
           P+  V IA LA+++GN ++L+GGKE + SN ++ +VI  AI  + +    + L+ + D  
Sbjct: 131 PNVTVDIAVLALKTGNAVILRGGKETLESNKLISEVIRGAIASQGLPVDAVQLIDSPDRA 190

Query: 474 -IADLLKLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIV 532
            +  LLKLD  +D+++PRG   L         IPV+    GICH+Y+DK AD++ A  ++
Sbjct: 191 LVTGLLKLDQYVDMIVPRGGQALQRLCAEQATIPVILGGIGICHLYVDKHADLERALEVI 250

Query: 533 MDAKIDYPAACNAMETLLVHKDLMKS--PGLDDILVALKTEGVNIYGGPIAHKALGFPKA 590
            +AK+  P  CNA++TLLV   + +   P + + L  L                LGF  +
Sbjct: 251 ANAKVQRPTVCNALDTLLVDTAVAERFVPQIAEYLHRLGVRFSVCEQSYALLDGLGFDIS 310

Query: 591 V----SFHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSA 646
                SF  E+ S+   ++ V D+ +AI HI  Y S H++ I+T D  VA  F+  V+SA
Sbjct: 311 PATEQSFATEWLSLTLGIKVVSDIDTAIAHIRTYSSGHSEAILTDDIHVATHFMNEVNSA 370

Query: 647 AVFHNASTRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRG 695
           AV+ NASTRF+DG +FGLGAEV +ST ++HARGP+G+E L T +W+  G
Sbjct: 371 AVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWLAWG 419


Lambda     K      H
   0.317    0.134    0.377 

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: 603
Number of extensions: 29
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: 716
Length of database: 425
Length adjustment: 36
Effective length of query: 680
Effective length of database: 389
Effective search space:   264520
Effective search space used:   264520
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