GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Bacteroides thetaiotaomicron VPI-5482

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate 349730 BT0202 histidinol-phosphate aminotransferase (NCBI ptt file)

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



>FitnessBrowser__Btheta:349730
          Length = 346

 Score =  147 bits (370), Expect = 6e-40
 Identities = 110/352 (31%), Positives = 182/352 (51%), Gaps = 30/352 (8%)

Query: 20  KPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALS 79
           KP S    E+    A++  L +NENP  +P +             RYPD   +ELK  LS
Sbjct: 16  KPYSSARDEYKGAVASVF-LDANENPYNLPHN-------------RYPDPMQWELKTLLS 61

Query: 80  ERYGVPADWVTLGNGSNDILEIAAHAFVE-KGQSIVYAQYSFAVYALATQ--GLGARAIV 136
           +   V    + LGNGS++ +++   AF E +  ++V    ++ +Y +      +  R ++
Sbjct: 62  KIKKVSPQHIFLGNGSDEAIDLVFRAFCEPEKDNVVAIDPTYGMYQVCADVNNVEYRKVL 121

Query: 137 VPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEA 196
           +    +    + +LAA  + T+LIF+ +PNNPTG  +   ++E  L +     +V+LDEA
Sbjct: 122 LDE-NFQFSAEKLLAATDERTKLIFLCSPNNPTGNDLLRSEIEKILREFEG--LVILDEA 178

Query: 197 YTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPF 256
           Y ++       + +    +YPNL+V +TFSKA+G A +R+G A A   +  +L++++ P+
Sbjct: 179 YNDFSEAPSFLEELD---KYPNLVVFQTFSKAWGCAAIRLGMAFASEAIIGILSKIKYPY 235

Query: 257 NVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLG--LEYVPSDGNFVLVRVG 314
           NVN L Q  AIA L+    +E+      +    L E F KL   +   PSD NF L +V 
Sbjct: 236 NVNQLTQQQAIAMLHKYYEIERWIKTLKEERDYLEEEFAKLSCTVRMYPSDSNFFLAKV- 294

Query: 315 NDDAAGNRVNLELLKQGVIVRPVGNYGL-PQWLRITIGLPEENEAFIAALER 365
             DA   ++   L+ +G+IVR   +  L    LR+T+G   EN   +AAL++
Sbjct: 295 -TDAV--KIYNYLVGEGIIVRNRHSISLCCNCLRVTVGTRVENNTLLAALKK 343


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: 304
Number of extensions: 22
Number of successful extensions: 4
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: 346
Length adjustment: 29
Effective length of query: 341
Effective length of database: 317
Effective search space:   108097
Effective search space used:   108097
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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