GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Rhodospirillum centenum SW SW; ATCC 51521

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_012569197.1 RC1_RS19545 histidinol-phosphate transaminase

Query= reanno::BFirm:BPHYT_RS14905
         (370 letters)



>NCBI__GCF_000016185.1:WP_012569197.1
          Length = 362

 Score =  252 bits (643), Expect = 1e-71
 Identities = 140/351 (39%), Positives = 197/351 (56%), Gaps = 7/351 (1%)

Query: 13  IAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDANAF 72
           IAPY+ G+  +            +++LASNE  LG    A  A      E+ RYPD  + 
Sbjct: 13  IAPYVGGEHSAPGVTR-------LLRLASNEGALGPSPRAVEAFRAVGPEIHRYPDGGST 65

Query: 73  ELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGA 132
            L+ A+  R+G+    V   NGS+++L + A A+   G  ++Y+++ F VY +A +  GA
Sbjct: 66  RLREAIGHRFGLDPARVLCFNGSDEVLHLLAQAYAGPGGEVLYSRHGFLVYPIAARAAGA 125

Query: 133 RAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVV 192
             +  P      D+DA+LA VS+ TR+++VANPNNPTG+++    L      +P HV++V
Sbjct: 126 TPVAAPERNLTTDVDALLARVSERTRIVYVANPNNPTGSYLPADALARLHAGLPPHVLLV 185

Query: 193 LDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRV 252
           +D AY EY+      D  A V R+ N++++RTFSK FGL G+R+G+A   P + D L+RV
Sbjct: 186 IDAAYAEYVTANDYADGTALVARFDNVVMTRTFSKLFGLGGMRLGWAYCPPAVADALHRV 245

Query: 253 RQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVR 312
           R PFNV+  AQAA +AAL D  F E+S ALN Q     T     LGL   PS  NFVLV 
Sbjct: 246 RSPFNVSVAAQAAGVAALEDLEFQERSRALNEQSRTAFTGRVRALGLVVHPSVCNFVLVD 305

Query: 313 VGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAAL 363
                         L  +G++VR +G YGLP  LRIT+GLP E E    AL
Sbjct: 306 FAATGRPAEEARQFLKARGILVRQMGAYGLPDCLRITMGLPAEMEEVADAL 356


Lambda     K      H
   0.318    0.135    0.385 

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: 349
Number of extensions: 8
Number of successful extensions: 1
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: 370
Length of database: 362
Length adjustment: 30
Effective length of query: 340
Effective length of database: 332
Effective search space:   112880
Effective search space used:   112880
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: 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