GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisA in Paraburkholderia bryophila 376MFSha3.1

Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate H281DRAFT_05659 H281DRAFT_05659 imidazole glycerol phosphate synthase subunit hisF

Query= curated2:Q3ZYM9
         (244 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05659 H281DRAFT_05659
           imidazole glycerol phosphate synthase subunit hisF
          Length = 257

 Score =  133 bits (334), Expect = 4e-36
 Identities = 82/231 (35%), Positives = 129/231 (55%), Gaps = 13/231 (5%)

Query: 10  IIPAIDILGGRCVRLFQGDYAQETVYSSDPVGTAMRWQSLGAPRLHVVDLDGAADGQSVN 69
           IIP +D+  GR V+   G    E   + DPV  A R+   GA  L  +D+   +D + + 
Sbjct: 7   IIPCLDVTAGRVVK---GVNFVELRDAGDPVEIARRYDDQGADELTFLDITATSDQRDLI 63

Query: 70  FELIKEIANSALIPVEVGGGIRSMETVKKLLVAGVDRVILGTAAVENPELVKEICARY-A 128
             +I+ +A+   IP+ VGGG+R++E V++LL AG D++ + ++AV NP+LVK+   +Y +
Sbjct: 64  LPIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKISMNSSAVANPQLVKDATDKYGS 123

Query: 129 DSVAVSIDAR---------NGKVATRGWVTNTEIDALELARSMKKLGIRRFIYTDISRDG 179
             + V+IDA+           +V T G    T ++A+E AR M +LG    + T + RDG
Sbjct: 124 QCIVVAIDAKRVSADGETPRWEVFTHGGRKATGLEAVEWARKMAELGAGEILLTSMDRDG 183

Query: 180 TLSEPNFAAIRDLISAINVPVIASGGVSSLSHLRLLKDIGAEGAIVGKAIY 230
           T S  + A  R +  A+ VPVIASGGV +L HL      G   A++  +I+
Sbjct: 184 TKSGFDLALTRAVSDAVPVPVIASGGVGNLQHLADGITSGHADAVLAASIF 234



 Score = 26.2 bits (56), Expect = 7e-04
 Identities = 16/98 (16%), Positives = 40/98 (40%)

Query: 38  DPVGTAMRWQSLGAPRLHVVDLDGAADGQSVNFELIKEIANSALIPVEVGGGIRSMETVK 97
           + V  A +   LGA  + +  +D        +  L + ++++  +PV   GG+ +++ + 
Sbjct: 158 EAVEWARKMAELGAGEILLTSMDRDGTKSGFDLALTRAVSDAVPVPVIASGGVGNLQHLA 217

Query: 98  KLLVAGVDRVILGTAAVENPELVKEICARYADSVAVSI 135
             + +G    +L  +     E       R+     +S+
Sbjct: 218 DGITSGHADAVLAASIFHYGEHTVGEAKRFMAEQGISV 255


Lambda     K      H
   0.319    0.137    0.386 

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: 175
Number of extensions: 12
Number of successful extensions: 5
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: 244
Length of database: 257
Length adjustment: 24
Effective length of query: 220
Effective length of database: 233
Effective search space:    51260
Effective search space used:    51260
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: 46 (22.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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