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

GapMind for Amino acid biosynthesis

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

Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate 352902 BT3375 aspartate aminotransferase (NCBI ptt file)

Query= SwissProt::H3ZPU1
         (389 letters)



>FitnessBrowser__Btheta:352902
          Length = 386

 Score =  287 bits (734), Expect = 4e-82
 Identities = 141/383 (36%), Positives = 238/383 (62%), Gaps = 3/383 (0%)

Query: 3   LSDRLEMVNPSEIRKLFDLAQGIEGIISLGIGEPDFDTPEHIKEYAKEALDKGLTHYSPN 62
           LS+    ++PS  R+LF+LAQ  + +I   +G+PD    + IKE   +A+ +G T YSPN
Sbjct: 4   LSEITNSISPSLTRRLFNLAQKYDNVIDFTLGDPDIHPHDKIKEAGCKAILEGRTRYSPN 63

Query: 63  IGILELREAVAEKFKKHNGIDADPKTQIMITVGTNQQILMGLATFLKDNEEVLIPSPMFV 122
            G+LELRE ++ ++K    I+ +P  +IM+TVG  + + + L   L   +EV+IP+P ++
Sbjct: 64  AGLLELREIISSRYKLQYNIEYNPTNEIMVTVGGMEGLYLTLLAILNRGDEVIIPAPYWI 123

Query: 123 SYAPAVILAGGKPVEVPTYEENEFRLSVDELEKYVTPKTRALIINTPNNPTGAVLTKKDL 182
           +Y   V +  G+P+       N+  +S++ + K +TPKT+A+I+NTP+NP+G +++   +
Sbjct: 124 NYVQMVCMCSGEPIITAPVSTNDLSISIENIRKAITPKTKAIILNTPSNPSGRIISDDSI 183

Query: 183 EEIADFAVEHDLMILSDEVYEYFVYDGVKNYSIASLDGMFERTITMNGFSKTFAMTGWRL 242
           ++IA  A+E+DL++++DEVY+  +YD     SI + D M ERT+ +N  SK F MTGWRL
Sbjct: 184 QQIAQIAIENDLIVITDEVYKTLLYDNAHFKSIVTCDKMKERTVVINSLSKEFCMTGWRL 243

Query: 243 GFLAAPEWVVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREYERRRNLVW 302
           G++AAP  ++  M  FQ   A C     QYAA +ALR+   + A   M  E+  RRN++ 
Sbjct: 244 GYIAAPSELISVMTMFQENIAACAPLPSQYAAIEALRNSEKYSA--GMIEEFTLRRNVLL 301

Query: 303 KRLNEMGLPTV-KPKGAFYIFPRIKDTGLSSKEFSELMIKEAKVVVVPGSAFGQAGEGYV 361
           + + ++   TV  P+G FY    IK TGL S+EF+  ++++ +V VVPG  +G   E ++
Sbjct: 302 EEVAKIKTITVDAPQGTFYAMLNIKSTGLKSEEFAYALLEKEQVAVVPGITYGDCCEDFI 361

Query: 362 RISYATAYEKLEEAMDRMEKVLK 384
           RI++     K++E + R+++ ++
Sbjct: 362 RIAFTLDIYKIKEGIQRLKRFVE 384


Lambda     K      H
   0.318    0.135    0.387 

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: 356
Number of extensions: 11
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: 389
Length of database: 386
Length adjustment: 30
Effective length of query: 359
Effective length of database: 356
Effective search space:   127804
Effective search space used:   127804
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: 50 (23.9 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for Amino acid biosynthesis