GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Thioalkalivibrio paradoxus ARh 1

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_006746920.1 THITH_RS15380 indole-3-glycerol phosphate synthase TrpC

Query= BRENDA::P00909
         (453 letters)



>NCBI__GCF_000227685.2:WP_006746920.1
          Length = 275

 Score =  161 bits (407), Expect = 3e-44
 Identities = 103/257 (40%), Positives = 144/257 (56%), Gaps = 8/257 (3%)

Query: 5   VLAKIVADKAIWVEARKQQQPLASFQNEVQPST--RHFYDALQG----ARTAFILECKKA 58
           +L +I+A K   + AR    PL    +  + +   R F  AL         A I E KKA
Sbjct: 11  ILQRILARKQEEIRARSATLPLPELASRARDADPPRGFRAALAARIRRGLPAVIAEIKKA 70

Query: 59  SPSKGVIRDDFDPARIAAIY-KHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDF 117
           SPSKGV+R DFDP  IA  Y +H A+ +SVLTD  +FQG+  +L         P+L KDF
Sbjct: 71  SPSKGVLRADFDPVAIAGSYARHGAACLSVLTDIDFFQGADGYLQKARAACDLPVLRKDF 130

Query: 118 IIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIAL 177
           ++DPYQ++ AR   AD  LL+++ LDD+Q R L  +A  L M VL EV + +E  RA+AL
Sbjct: 131 VVDPYQVHEARALGADCILLIVAALDDEQMRALYRLALDLGMDVLVEVHDRDELGRALAL 190

Query: 178 GAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQV-RELSHFANGFLI 236
            A ++GINNRDLR     L  T +L  ++   V +++ESGI+  + V R  +     FL+
Sbjct: 191 DAGLIGINNRDLRSFETRLETTLDLCAQVPEGVLLVTESGIHRPSDVARMRAAGVEAFLV 250

Query: 237 GSALMAHDDLHAAVRRV 253
           G A M   D   A+ R+
Sbjct: 251 GEAFMRAPDPGEALERL 267


Lambda     K      H
   0.320    0.135    0.389 

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: 255
Number of extensions: 15
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: 453
Length of database: 275
Length adjustment: 29
Effective length of query: 424
Effective length of database: 246
Effective search space:   104304
Effective search space used:   104304
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: 49 (23.5 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