GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Shewanella sp. ANA-3

Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate 7022920 Shewana3_0170 3'(2'),5'-bisphosphate nucleotidase (RefSeq)

Query= SwissProt::P95189
         (260 letters)



>FitnessBrowser__ANA3:7022920
          Length = 270

 Score = 82.0 bits (201), Expect = 1e-20
 Identities = 69/224 (30%), Positives = 96/224 (42%), Gaps = 7/224 (3%)

Query: 10  LALADRADELTRVRFGALDLRIDTKPDLTPVTDADRAVESDVRQTLGRDRPGDGVLGEEF 69
           +A+A  A    R  +   +   +TK D TPVT AD A    + + L    P   +L EE 
Sbjct: 11  IAIATDAGRTIREIYLKGNFERETKSDNTPVTSADLAANQLICERLAALTPDIPILSEEA 70

Query: 70  GGSTTFTG----RQWIVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQRRWW 125
                       R W+VDP+DGT  F+ G   ++ +IAL+E   P +GVV  P  Q  ++
Sbjct: 71  ADIPLSVREGWKRYWLVDPLDGTGEFIAGSGDFSVIIALVEHNRPVMGVVYVPMTQVCYY 130

Query: 126 AARGRGAFASVDGARPHRLSVSSVAELHSASLSFSSLSGWARPGLRERFIGLTDTVWRVR 185
           A  G GA+   D  +  R+S   +      SL   ++S    P               V 
Sbjct: 131 AIAGLGAYKRTD-KQEVRISSRQIQHREQVSLRL-AVSRRQDPQSVLTLFNQPKHCELVV 188

Query: 186 AYGDFLSYCLVAEGAVDIAAE-PQVSVWDLAALDIVVREAGGRL 228
             G  L  CLVAEG  D          WD  A  I++ EAGG+L
Sbjct: 189 MGGAALKSCLVAEGRADCYVRVGPTGEWDTGAAQIIIEEAGGQL 232


Lambda     K      H
   0.319    0.136    0.414 

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: 127
Number of extensions: 6
Number of successful extensions: 4
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: 260
Length of database: 270
Length adjustment: 25
Effective length of query: 235
Effective length of database: 245
Effective search space:    57575
Effective search space used:    57575
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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