GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvH in Magnetospirillum magneticum AMB-1

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011384931.1 AMB_RS12840 thiamine pyrophosphate protein

Query= curated2:Q7U5G1
         (617 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384931.1 AMB_RS12840 thiamine
           pyrophosphate protein
          Length = 561

 Score =  244 bits (624), Expect = 5e-69
 Identities = 174/521 (33%), Positives = 260/521 (49%), Gaps = 31/521 (5%)

Query: 17  APQTISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTH 76
           AP+T  G   L DAL   G DT+   PG + LP  DA    +    +K +  RHE    +
Sbjct: 7   APRT--GGEILADALLAQGADTVTCVPGESFLPFLDAAW--DRRDRLKVLAFRHEGGAAY 62

Query: 77  AADAYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQET 136
           AA+A+ + TG+ GVC    GPGAT+   G+ TA  DS PMV++ GQV RP  G +AFQE 
Sbjct: 63  AAEAHGKLTGRPGVCIVGRGPGATHASVGVHTAFQDSTPMVLLIGQVDRPIRGREAFQEV 122

Query: 137 DIFGITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVE 196
           ++  +  P+ K    +  P  L   VA+AF  A  GRPGP ++ +P+D+  E+ +   VE
Sbjct: 123 ELAQMFRPLAKRVEEITSPDRLPEAVARAFAAAMGGRPGPAVLILPEDMLAERASVADVE 182

Query: 197 PGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLP 256
               +P     P P     +   ++L+ +A+RPL+ VGGG  +  A   +   AE + LP
Sbjct: 183 R---LPPALPHPGP---CRLDKMVELLAKARRPLMLVGGGGWTPEAARLITAFAEGWSLP 236

Query: 257 VTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVT---GKLDT 313
           V      +   D   A   G LG          V E DL++AVG R  D  T     ++ 
Sbjct: 237 VAACFRRQDIVDNESACYGGELGYSMAPSLGARVREADLILAVGTRLGDIDTAGYSLIEA 296

Query: 314 FAPRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLE---- 369
             P+  ++H   +  E+G+  + D+A++  + L  AR       + A P    W +    
Sbjct: 297 PNPKQILIHVFPEAEELGRVFRPDLAIVSAM-LPFARRA----SQLAAPAALPWTDWTRA 351

Query: 370 -RINTWKDRYPLTIPPAEGAIYPQEVLLAVRDLAP-DAIVTTDVGQHQMWAAQ-HLRNGP 426
            R +   +R P + P   GA+   +V+  +    P DAI+ T  G +  W  + H     
Sbjct: 352 VRGDHLANRVPNSCP---GALDMGQVMAEIEARLPEDAIICTGAGNYTGWPQRFHRFRRY 408

Query: 427 RGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVV 486
            G ++ A  G+MG+G+PAA+ A+   PDR VV  AGD   LM  QEL T   +GL   V+
Sbjct: 409 PGQLAPAN-GSMGYGLPAALAAKALYPDRAVVAFAGDGCFLMTAQELATAKLHGLSPVVL 467

Query: 487 IVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSF 527
           +V+N   G +R  QE+ +  R  A+D+ N  PDF ALA ++
Sbjct: 468 VVDNGMYGTIRMHQEASHPGRTLATDLAN--PDFAALAAAY 506


Lambda     K      H
   0.320    0.136    0.414 

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: 948
Number of extensions: 46
Number of successful extensions: 4
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: 617
Length of database: 561
Length adjustment: 37
Effective length of query: 580
Effective length of database: 524
Effective search space:   303920
Effective search space used:   303920
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 (21.8 bits)
S2: 53 (25.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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