GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Magnetospirillum magneticum AMB-1

Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_011383697.1 AMB_RS06545 inositol monophosphatase

Query= curated2:P56160
         (259 letters)



>NCBI__GCF_000009985.1:WP_011383697.1
          Length = 265

 Score =  115 bits (287), Expect = 1e-30
 Identities = 82/251 (32%), Positives = 129/251 (51%), Gaps = 7/251 (2%)

Query: 5   LQLALELAEKAGK-LTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPDDGL 63
           L + +  A KA + L  DY     LQV  K     V+ AD   E+ +R  +    P  G 
Sbjct: 8   LNVMMGAARKAARNLVRDYGEVEHLQVSKKGPADFVSSADIKTEKTLRAELKKARPGFGF 67

Query: 64  FGEEFDEHPSGN-GRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALGEL 122
             EE  E    +   RWIIDPIDGT +F+HG+P + + IALE +G +  GV+  P   E+
Sbjct: 68  LMEEGGEIAGDDTSHRWIIDPIDGTTNFLHGIPNFCISIALERDGELFAGVVYQPLGDEM 127

Query: 123 YQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVDQLRI----DAGLV 178
           + AE+G+GAF+N   ++VSA       T++ T   ++  P     + +L       AG+ 
Sbjct: 128 FHAEKGAGAFLNERRLRVSA-RRKLEDTLIATGIPFIGRPGHETFLKELGAVMPQVAGIR 186

Query: 179 RGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGLV 238
           R          VA+GR +   +  + PWD AA I +V+EAGG   D++G   ++D   ++
Sbjct: 187 RFGSAALDLAYVAAGRCDGYWETGIKPWDIAAGIVLVKEAGGYVTDFQGGSKMLDNGEVL 246

Query: 239 SANNAMGRNLI 249
           +AN+ + + L+
Sbjct: 247 AANDHLHQPLM 257


Lambda     K      H
   0.319    0.138    0.415 

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: 159
Number of extensions: 12
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: 259
Length of database: 265
Length adjustment: 25
Effective length of query: 234
Effective length of database: 240
Effective search space:    56160
Effective search space used:    56160
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 (21.7 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