GapMind for Amino acid biosynthesis

 

Alignments 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:Q3Z6V7
         (237 letters)



>FitnessBrowser__Burk376:H281DRAFT_05659
          Length = 257

 Score =  129 bits (325), Expect = 4e-35
 Identities = 79/231 (34%), Positives = 127/231 (54%), Gaps = 13/231 (5%)

Query: 3   IIPAIDILGGRCVRLLQGDYAQETVYSPDPVGTAMRWQSLGAPRLHVVDLDGAADGESVN 62
           IIP +D+  GR V+   G    E   + DPV  A R+   GA  L  +D+   +D   + 
Sbjct: 7   IIPCLDVTAGRVVK---GVNFVELRDAGDPVEIARRYDDQGADELTFLDITATSDQRDLI 63

Query: 63  FELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICARY-A 121
             +I  +A+   IP+ VGGG+R+++ V++LL AG D++ + + AV NP+LV++   +Y +
Sbjct: 64  LPIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKISMNSSAVANPQLVKDATDKYGS 123

Query: 122 DSVAVSIDAR---------NGKVATRGWVNSTEVDALELARSMKKLGVKRFIYTDISRDG 172
             + V+IDA+           +V T G   +T ++A+E AR M +LG    + T + RDG
Sbjct: 124 QCIVVAIDAKRVSADGETPRWEVFTHGGRKATGLEAVEWARKMAELGAGEILLTSMDRDG 183

Query: 173 TLSEPNFAAIRDLISAINMPVIASGGVSSLSHLRLLKDIGAEGAIVGKAIY 223
           T S  + A  R +  A+ +PVIASGGV +L HL      G   A++  +I+
Sbjct: 184 TKSGFDLALTRAVSDAVPVPVIASGGVGNLQHLADGITSGHADAVLAASIF 234


Lambda     K      H
   0.318    0.136    0.384 

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: 176
Number of extensions: 15
Number of successful extensions: 5
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: 237
Length of database: 257
Length adjustment: 24
Effective length of query: 213
Effective length of database: 233
Effective search space:    49629
Effective search space used:    49629
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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