GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Azorhizobium caulinodans ORS 571

Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_081433973.1 AZC_RS12315 3'(2'),5'-bisphosphate nucleotidase CysQ

Query= BRENDA::Q8NS80
         (260 letters)



>NCBI__GCF_000010525.1:WP_081433973.1
          Length = 279

 Score =  103 bits (258), Expect = 3e-27
 Identities = 87/261 (33%), Positives = 123/261 (47%), Gaps = 31/261 (11%)

Query: 10  LALELAELADSITLDRFEASDLEVSSKPDMTPVSDADLATEEALREKIATARPADSILGE 69
           L  +    A +I LD F A  LE  SK + +PV+ AD+A +  L+++     P    L E
Sbjct: 25  LMADAVTAAGAIALDMFRAGRLESWSKANDSPVTAADIAVDRFLKDRFTALAPDYGWLSE 84

Query: 70  EF--GGDVEFSGRQWIIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISAPALARRWW 127
           E     D     R W++DPIDGT+ ++ G   WA   AL++NG+PVA  + APA    + 
Sbjct: 85  ESVDSPDRLARSRVWVVDPIDGTRGFMAGGVDWAVSAALVENGRPVAAALFAPASEELFV 144

Query: 128 ASEGAGAWRTFNGSSPRKLSVSQVSKLDDASLS--FSSLSGWAERDLRDQFVSLTDTTWR 185
           AS GAGA R  NG     L+VS ++ L  A +S   +SL   A+    ++   +     R
Sbjct: 145 ASVGAGATR--NGV---PLAVSDLTALAGARISGPVASLDRLAQHAPIERRPRVRSLALR 199

Query: 186 LRGYGDFFSYCLVAEGAVDIA-AEPEVSLWDLAPLSILVTEAGGKFTSLAGVDG------ 238
           +           VA   +D+A A P    WD+A   +LV EAGG    L+G+DG      
Sbjct: 200 I---------TRVATAELDVALAAPNAHDWDIAAADLLVQEAGG---LLSGLDGRPLTYN 247

Query: 239 ---PHGGDAVATNGILHDETL 256
              P  G  V     LH   L
Sbjct: 248 ATVPRHGALVCAGTALHPHIL 268


Lambda     K      H
   0.315    0.133    0.396 

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: 230
Number of extensions: 13
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: 260
Length of database: 279
Length adjustment: 25
Effective length of query: 235
Effective length of database: 254
Effective search space:    59690
Effective search space used:    59690
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: 47 (22.7 bits)

This GapMind analysis is from Jul 25 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