GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Marinobacter adhaerens HP15

Align Histidinol-phosphatase; HolPase; Histidinol-phosphate phosphatase; EC 3.1.3.15 (characterized)
to candidate GFF2461 HP15_2405 3'(2'), 5'-bisphosphate nucleotidase

Query= SwissProt::P95189
         (260 letters)



>FitnessBrowser__Marino:GFF2461
          Length = 258

 Score = 96.3 bits (238), Expect = 6e-25
 Identities = 76/233 (32%), Positives = 110/233 (47%), Gaps = 20/233 (8%)

Query: 10  LALADRADELTRVRFGALDLRIDTKPDLTPVTDADRAVESDVR---QTLGRDRPGDGVLG 66
           + +AD A E   +     D ++  K D +P+T AD A    +    +++ RD P   +L 
Sbjct: 11  IKVADAASEKV-LHIYQSDFKVSYKADASPITAADTAAHDIITHGLRSISRDIP---ILS 66

Query: 67  EEFGGSTTFTGRQ-----WIVDPIDGTKNFVRGVPVWASLIALLEDGVPSVGVVSAPALQ 121
           EE G    +  R+     W+VDP+DGTK+F +    +   IA++EDG P +GVV APAL+
Sbjct: 67  EE-GSDIPWEERKHWRRFWLVDPVDGTKDFTQRTGEFTVNIAMIEDGQPVMGVVIAPALK 125

Query: 122 RRWWAARGRGAFASVDGARPHRLSVSSVAELHSASLSFSSLSGWARPGLRERFIGLTDTV 181
             +W   G GA       R H + V+    L     S + L+   R      FI      
Sbjct: 126 EAFWGIVGEGAHMRDRTGRVHHIRVAEPKPLKRVVASKNHLNEETR-----AFIEALGDH 180

Query: 182 WRVRAYGDFLSYCLVAEGAVDIAAE-PQVSVWDLAALDIVVREAGGRLTSLDG 233
             V+A G  L  C +AEG  DI       S WD  A   V+  AGG++ +LDG
Sbjct: 181 ELVQA-GSSLKLCRIAEGHADIYPRLGPTSEWDTGAAQAVLMAAGGKVQTLDG 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: 136
Number of extensions: 5
Number of successful extensions: 2
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: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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.

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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