GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__ANA3:7023725
          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:

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