GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hcs in Pedobacter sp. GW460-11-11-14-LB5

Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate CA265_RS15855 CA265_RS15855 2-isopropylmalate synthase

Query= BRENDA::D0VY45
         (540 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS15855 CA265_RS15855
           2-isopropylmalate synthase
          Length = 386

 Score =  340 bits (872), Expect = 6e-98
 Identities = 189/397 (47%), Positives = 256/397 (64%), Gaps = 17/397 (4%)

Query: 18  HIPNPTYVRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMA 77
           H PN  Y  I DTTLRDGEQ PG  +   QK+E A+ L  LGVD+IEAGFP +S  DF +
Sbjct: 3   HDPNKVY--IFDTTLRDGEQVPGCQLDTNQKVEIAKSLELLGVDVIEAGFPVSSPGDFNS 60

Query: 78  VKMIAEEVGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEY 137
           V  +++ V N        P+I  ++R N+ DI  A +AL++AKRPR+ T I +S  H+++
Sbjct: 61  VIELSKAVTN--------PIICALTRANKNDIDVAADALRYAKRPRIHTGIGSSDFHIKH 112

Query: 138 KLRKSKDQVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTI 197
           K   +++++LE A   V++++     D++F AEDA R+D EFL ++   VI AGAT + I
Sbjct: 113 KFNSTREEILERAVEAVRYSKKF-VEDVEFYAEDAGRADIEFLAKMVEAVIAAGATVVNI 171

Query: 198 PDTVGIAMPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVT 257
           PDT G  +P +YG  I  +K N   I+ AI++ HCHNDLGLATAN+I G + GARQ+E T
Sbjct: 172 PDTNGYCLPDQYGSKILFLKENVKNIDKAIISVHCHNDLGLATANSIAGLQNGARQVECT 231

Query: 258 INGIGERAGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKA 317
           INGIGERAGN S EEVVM L    I    GL+T I+     + S MV     + +QP+KA
Sbjct: 232 INGIGERAGNTSMEEVVMILKTHKI---LGLNTQIDATRFYEMSHMVRNQMNMPVQPNKA 288

Query: 318 LVGANAFLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEE 377
           +VG NAF H SGIHQDG LK+R  YEII PED+G   +   TIVL   SGR AL++ L+ 
Sbjct: 289 IVGGNAFSHSSGIHQDGFLKNRENYEIIKPEDVGFPDA---TIVLTARSGRHALKHHLDR 345

Query: 378 LGYKLKDTEVEGVFWQFKAVAEKKKRITDTDLRALVS 414
           LG+KL+   ++ V+ QF  +A+ K+ I D DL  LV+
Sbjct: 346 LGHKLEKDHLDIVYKQFLVLADSKQGINDQDLNQLVA 382


Lambda     K      H
   0.318    0.134    0.390 

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: 527
Number of extensions: 19
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 540
Length of database: 386
Length adjustment: 33
Effective length of query: 507
Effective length of database: 353
Effective search space:   178971
Effective search space used:   178971
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: 51 (24.3 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 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