GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Xenophilus azovorans DSM 13620

Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_038201147.1 Q392_RS03145 acetolactate synthase large subunit

Query= curated2:O53554
         (515 letters)



>NCBI__GCF_000745855.1:WP_038201147.1
          Length = 520

 Score =  456 bits (1174), Expect = e-133
 Identities = 258/521 (49%), Positives = 327/521 (62%), Gaps = 12/521 (2%)

Query: 1   MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60
           MNGA++L++TL+D GVD CFANPGTSEMHFV+ALD +  MR +L LFEGV TGAADGY R
Sbjct: 1   MNGAESLVHTLLDAGVDTCFANPGTSEMHFVSALDRIAGMRCVLGLFEGVVTGAADGYYR 60

Query: 61  IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120
           +AGRPAA LLHLGPGL NGLANLHNA++AR  +V VVG+HAT H   DAPL SDI  +A 
Sbjct: 61  MAGRPAATLLHLGPGLANGLANLHNAKKARSGIVNVVGEHATTHLALDAPLTSDIQGLAV 120

Query: 121 TVSGWVRRTEAAADVGADA-EAAIAASRSGSQIATLILPADVCWSDGAHA--AAGVPAQA 177
            +S WVR   +A  + +D  EA + AS    ++ATL LPAD+ WSD A A  A G   + 
Sbjct: 121 PMSHWVRTVRSADAIASDCREAVVQASGRPGRVATLALPADMAWSDTAAAPPALGAVREP 180

Query: 178 AAAPVDVGPVAG----VLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTC 233
            A PV+   V      + R G   ++L+GG A R      A RI  ATG   + E +   
Sbjct: 181 VALPVEQEAVIAAARILRRHGGSTLLLLGGRAVRARATEWAGRIAAATGCAVMSEFYAER 240

Query: 234 LERGAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHV 293
           +ERGAG   V RL Y  +GA   L    H+VL GA  PV+FF YP  P  L   G     
Sbjct: 241 IERGAGRVPVPRLPYAVQGAVDALSRFDHIVLVGAAEPVAFFGYPDKPGRLAAPGTTFAT 300

Query: 294 LA-EPGGAADALAALADEVAPGTVAPVA---GASRPQLPTGDLTSVSAADVVGALLPERA 349
           L+      A AL  + +E+    V P      A+  +L  G +T  S   ++ AL+PE A
Sbjct: 301 LSTHAQDPAQALRMVCEELGAMRVNPATCGRAAAHAELEEGPVTPASIGALLAALIPENA 360

Query: 350 IVVDESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGS 409
           IVVDE+ + G      T  A  HDWLT  GG+IGYG+P AVGAA+AAP R VL LE DGS
Sbjct: 361 IVVDEAISTGRAFDATTRDAAPHDWLTNMGGSIGYGLPVAVGAAIAAPGRRVLALEGDGS 420

Query: 410 AMYTISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMD 469
           AMYT+  LW+ ARE+L+VT V++ N +Y ILR E  +VGAGS PG +A D+L I RP +D
Sbjct: 421 AMYTLQALWTMARESLNVTVVVFANRSYQILRGEYAQVGAGS-PGRRAGDMLGIDRPALD 479

Query: 470 FVKIAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510
           +V +A G GVPA RV+T  +F DA+R A A  GP L+++V+
Sbjct: 480 WVALASGQGVPACRVSTLGQFGDAVRRANATEGPSLVELVL 520


Lambda     K      H
   0.318    0.134    0.402 

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: 694
Number of extensions: 33
Number of successful extensions: 5
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: 515
Length of database: 520
Length adjustment: 35
Effective length of query: 480
Effective length of database: 485
Effective search space:   232800
Effective search space used:   232800
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: 52 (24.6 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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