GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Thiohalospira halophila DSM 15071 HL 3

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_093428106.1 BM272_RS07235 acetolactate synthase large subunit

Query= curated2:O08353
         (599 letters)



>NCBI__GCF_900112605.1:WP_093428106.1
          Length = 543

 Score =  311 bits (797), Expect = 4e-89
 Identities = 189/564 (33%), Positives = 299/564 (53%), Gaps = 37/564 (6%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           M  AE  ++ LE E VE +FG PG   L   DAL  SD+  +  RHEQ AA  AD Y R 
Sbjct: 1   MKTAELFVRCLENEGVEYIFGLPGEENLDVMDALVDSDIQFITVRHEQGAAFMADVYGRL 60

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           +G+ GVC+ T GPGATNL+TGVA A+ D +P+VA+ GQ  T  +  ++ Q +D   LF P
Sbjct: 61  TGRAGVCLATLGPGATNLITGVADANMDHAPLVAIAGQASTNRLHKESHQVLDLQNLFRP 120

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
           + K++ ++       E+ R AF++AQ+ + G   I+ P+++   E+ I+  P+  +  + 
Sbjct: 121 VTKYSSRLLTPAITTEVVRKAFKLAQSEKTGACFIEFPENI--AEMPIEDEPLTVRQPVA 178

Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240
              P       +++ A   I++A  PIILAG GV+ SGA E L +  E +NIPV  T M 
Sbjct: 179 PEPPGD-----RVEAAAAAISAANNPIILAGNGVIRSGACEALAEFAEAMNIPVANTFMA 233

Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIG---CRFSDRITGDIKSFATNAKI 297
           KG I   HP+ALG  G+      +    ++D+++ IG     +   +    +S     ++
Sbjct: 234 KGAIPFKHPMALGSAGLQAKDYVSCGFDQADLVLCIGYDLVEYHPYLWNPTRS----NRL 289

Query: 298 IHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVN 357
           +HID  PAE+    +VDV +VGD    L+ + +       + ++           IE++N
Sbjct: 290 VHIDNTPAEVDAFYSVDVGVVGDITHSLQRIAEAATPRAGQFARPLR-----RALIEDMN 344

Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAV--IDDLNINKNTIITTDVGQNQMWMAHYFKT 415
              + S         P+KPQKI+ +L     +DD+ I        DVG ++MWMA  F+ 
Sbjct: 345 EHAEDS-------RFPVKPQKIIWDLRTAMQLDDIAI-------CDVGAHKMWMARMFRA 390

Query: 416 QTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPV 475
           + P + L S G   MG   P A+GA++A+P   V+ +TGD GF+MN QEL T     I +
Sbjct: 391 ERPNTCLISNGFAAMGIALPGAVGARLARPGVNVVAVTGDAGFLMNAQELETAVRQGISM 450

Query: 476 VICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEAL 535
           V+ ++++   G++ +W+ L    R  +V+F   PD +  A+S+G    RIE   ++   L
Sbjct: 451 VVLVWNDAGYGLI-EWKQLNAYGRTSAVDFNN-PDLVTFAQSFGAHGYRIERTEDLLPTL 508

Query: 536 KEAINCDEPYLLDFAIDPSSALSM 559
           +EA+      ++D  +D S  L +
Sbjct: 509 REALADGGVSVIDCPVDYSENLKL 532


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: 710
Number of extensions: 28
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: 543
Length adjustment: 36
Effective length of query: 563
Effective length of database: 507
Effective search space:   285441
Effective search space used:   285441
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 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