GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Lentibacillus jeotgali Grbi

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_029329105.1 ON01_RS12165 acetolactate synthase large subunit

Query= curated2:O08353
         (599 letters)



>NCBI__GCF_000224785.1:WP_029329105.1
          Length = 546

 Score =  319 bits (818), Expect = 2e-91
 Identities = 195/572 (34%), Positives = 303/572 (52%), Gaps = 32/572 (5%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           MN AE ++K LE E VE +FG PG   +   DA + SD+  ++TRHE +AA  A  Y R 
Sbjct: 4   MNVAELLVKCLEQEGVEYVFGVPGEENVDLMDAFYDSDIEFIVTRHETSAAFMAATYGRL 63

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           +G  GVC+ T GPGATNL+TGVA A+ D +P+VA+TGQ         + Q  D + ++ P
Sbjct: 64  TGTPGVCLATLGPGATNLMTGVANANMDHAPLVAITGQAGLDRQHKISHQYYDLINMYEP 123

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
           + K N QI+     PE+ R AF++A   + G  HIDLP+D+  ++++      P++    
Sbjct: 124 VTKWNAQIKSAKITPEVVRKAFQVAGQEKWGATHIDLPEDIAGMDIEKATPLNPNE---- 179

Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240
              P T      I++A+ +I  A+ P+ILAG G+    A EE    V  + IPV  + MG
Sbjct: 180 --RPHTKASESIIEQAVNMIEKAEHPLILAGNGISRQQATEEFRAFVRKVKIPVVHSFMG 237

Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300
           KG IS  + L+L   G+ G        +ESD++I++G   ++    +     +N +IIH+
Sbjct: 238 KGAISWENDLSLLTAGIGGNDYITCGFNESDLIITVGFDIAEYPPKNWN--RSNTQIIHL 295

Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENIS-QWIENVNSL 359
           D + AE   N  V + I+GD    L+++             EN +  N    W+ NV   
Sbjct: 296 DTEEAETDANYPVGLNILGDIPANLQQL------------GENIESPNADFAWVSNVRKQ 343

Query: 360 KKSSIPVMDYD-DIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418
             + +   + D   P+KPQKI+ +L  V     +N++ I  +DVG ++MWMA  + T  P
Sbjct: 344 ALNELEAFEEDTHFPVKPQKIISDLRKV-----LNEDAIAISDVGAHKMWMARMYHTHQP 398

Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478
            + L S GL +MG   PSAI AK+  PD  V+ + GDG F M   EL T     +P+++ 
Sbjct: 399 NTCLISNGLASMGVAVPSAIAAKMVHPDRNVVAVCGDGSFQMTGAELETARRLELPIIVL 458

Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538
           ++ +   G++ +W  L    R   + FG  PD+ +LA SYG +   I   +E+  AL++A
Sbjct: 459 MWRDDGYGLI-EWHQLKKFDRSSYIKFGN-PDYQQLAASYGFEVMTITKADELKPALEKA 516

Query: 539 INCDEPYLLDFAIDPSSALSMVPPGAKLTNII 570
              ++P  +D  +D S  + +     KL +II
Sbjct: 517 AASNQPTFIDCPVDYSENMKLT---EKLGDII 545


Lambda     K      H
   0.319    0.137    0.405 

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: 760
Number of extensions: 33
Number of successful extensions: 6
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: 599
Length of database: 546
Length adjustment: 36
Effective length of query: 563
Effective length of database: 510
Effective search space:   287130
Effective search space used:   287130
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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