GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Novosphingobium barchaimii LL02

Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_059149611.1 V474_RS00340 phosphoglycerate dehydrogenase

Query= reanno::Cola:Echvi_2777
         (630 letters)



>NCBI__GCF_001046635.1:WP_059149611.1
          Length = 527

 Score =  203 bits (517), Expect = 1e-56
 Identities = 123/368 (33%), Positives = 199/368 (54%), Gaps = 13/368 (3%)

Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294
           VL+ + + P    I  + G +V+V++   +E+++  +I     + IRS T++TK++L  A
Sbjct: 6   VLISDKMDPNAARIFTEMGCDVDVITGENAEQQIA-RIGEYDGLAIRSSTRVTKEMLAAA 64

Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354
             L  +G   IG + +D+     +G+ V N PF N+ +  E AI+ I  L R L +   +
Sbjct: 65  KNLKVIGRAGIGVDNVDIPAASSQGVVVMNTPFGNSITTAEHAIALIFALARQLPEANAQ 124

Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGNA 412
              G+W K+     EV GK LG+IG GNIG+ ++  A  + M V  +D  +    A+   
Sbjct: 125 TQAGLWPKNGFMGVEVTGKTLGLIGAGNIGSIVASRALGLRMKVVAFDPFLTPERAVEMG 184

Query: 413 TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRD 472
            +   L+ LL   D I+LH     + +NIL+ E + K KKG  +VN +RG ++D  AL+ 
Sbjct: 185 VEKADLETLLARADFITLHTPLTDQTRNILSAENLAKTKKGVRIVNCARGGLIDEAALKA 244

Query: 473 ALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGK 532
            L+SGH+AGAA+DVF TEP       +S L G PN I TPH+G ST EAQ N+A  V  +
Sbjct: 245 GLDSGHIAGAALDVFQTEPAK-----DSPLFGTPNFICTPHLGASTTEAQVNVALQVAEQ 299

Query: 533 IIEYINSGNTFNSVNFPNI---QLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIVG 589
           + +++ +G   N++N P++   + P LK   +L  +  +  G L      +    I++ G
Sbjct: 300 MADFLVNGGVTNALNMPSLSAEEAPKLKPYMKLAEVLGSMVGQLTV--DSVPRISIHVEG 357

Query: 590 QYLKTNEK 597
              + N+K
Sbjct: 358 AAAELNQK 365



 Score = 27.7 bits (60), Expect = 0.001
 Identities = 20/93 (21%), Positives = 45/93 (48%), Gaps = 11/93 (11%)

Query: 539 SGNTFNSVNFPNIQLPFLK-----DAHRLIHIHQNAPGVLAKINQVLASYKINI----VG 589
           +G  FN+V    +++  +K     D   L  ++++APG + +I  ++    INI    +G
Sbjct: 428 AGTLFNNVEPRLVEMFGIKVEAELDGSMLYIVNEDAPGFIGRIGTLMGEQGINIGTFNLG 487

Query: 590 QYLKTNEKIGYVITDIDKRYSNDVIDALKEIEG 622
           +     E +  ++  +D   + DV++  + + G
Sbjct: 488 RRTTGGEAV--LLLSVDTPVAADVLEQARALPG 518


Lambda     K      H
   0.317    0.136    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: 617
Number of extensions: 28
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 630
Length of database: 527
Length adjustment: 36
Effective length of query: 594
Effective length of database: 491
Effective search space:   291654
Effective search space used:   291654
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 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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