GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Desulfovibrio vulgaris Hildenborough

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate 208745 DVU3223 aspartate aminotransferase

Query= BRENDA::Q8YMS6
         (388 letters)



>MicrobesOnline__882:208745
          Length = 390

 Score =  353 bits (905), Expect = e-102
 Identities = 182/386 (47%), Positives = 251/386 (65%), Gaps = 4/386 (1%)

Query: 1   MKLAARVSQVTPSITLAIAAKAKAMKAEGIDVCSFSAGEPDFDTPAHIKAAAAKALDEGK 60
           M ++ R++++ PS TLA+ AKA  +KA G+ V S + GEPDF TPAHI  AA +A+DEG 
Sbjct: 1   MNISDRLTRIKPSATLAVNAKALELKARGVKVVSLAVGEPDFGTPAHICEAAKRAIDEGF 60

Query: 61  TKYGAAAGEPKLREAIARKLQKDNHLDYKPENVIVTNGGKHSLYNLIVALIDPGDEVIIP 120
           T+Y    G  +LREA+A    +   ++   E  IVTNGGK +LYNL  AL++PGDEV++P
Sbjct: 61  TRYTPVPGIIELREAVAGYFGRCYGVEAPAEATIVTNGGKQALYNLFQALLNPGDEVLVP 120

Query: 121 APYWLSYPEMVTLVGGKSVIVPTDASTGYKITPEQLRKAITPKTKLFVLNSPSNPTGMVY 180
           APYW+SYP +V L  G  V VP+ A  G+KITP +L    TP+T++ +LNSPSNPTG  Y
Sbjct: 121 APYWVSYPALVQLAEGVPVFVPSPAERGFKITPAELDAHRTPRTRVLLLNSPSNPTGACY 180

Query: 181 TPEEIKALAQVVVDADIYVVSDEIYEKILYDGAQHISIGSLGKEIFNRTLISNGFAKAYS 240
           T EE+ AL Q  VD DI+V++DEIY++++Y   Q +S+    +   +R  + NG AK ++
Sbjct: 181 TREEMDALMQWAVDHDIFVIADEIYDRLVYGDMQPVSVSGWWQRFPDRVAVVNGLAKTFA 240

Query: 241 MTGWRLGYLAGPVDIIKAASSIQGHSTSNVCTFAQYGAIAALEDSQDCVEEMRQAFAKRR 300
           MTGWR+GY+    D++KA + IQG STSN+C+ AQ  A+AAL    D VEEMR AF +RR
Sbjct: 241 MTGWRVGYVLAHPDLVKAVAKIQGQSTSNICSIAQKAALAALTGPYDAVEEMRCAFVRRR 300

Query: 301 QVMLDRLNAIPGLSTAKPDGAFYLFPDISK----TGLKSLEFCDALIEEHKVAVIPGIAF 356
            +  D ++    +   +PDGAFYLF DI +    +   S   C  L+EE +VA++PG AF
Sbjct: 301 DLAYDIISGWKDVVCPRPDGAFYLFADIHRHYNASMPDSAAVCTRLLEEAQVALVPGSAF 360

Query: 357 GADDNIRLSYATDLATIEKGLDRLEK 382
           G D  IR SYA     +E  L R+ K
Sbjct: 361 GDDKCIRFSYAVADDVLEDALSRVAK 386


Lambda     K      H
   0.317    0.134    0.381 

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: 402
Number of extensions: 19
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: 388
Length of database: 390
Length adjustment: 30
Effective length of query: 358
Effective length of database: 360
Effective search space:   128880
Effective search space used:   128880
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 (21.6 bits)
S2: 50 (23.9 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