GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS15855
          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.

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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