GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Phyllobacterium endophyticum PEPV15

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_106717976.1 CU100_RS14805 thiamine pyrophosphate-requiring protein

Query= BRENDA::P00893
         (574 letters)



>NCBI__GCF_003010935.1:WP_106717976.1
          Length = 555

 Score =  201 bits (512), Expect = 5e-56
 Identities = 170/559 (30%), Positives = 255/559 (45%), Gaps = 40/559 (7%)

Query: 2   EMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGL 61
           + +SGA++V   L  +G+KQ+ G+P   + D   A      I  V+ R  + AV++A+G 
Sbjct: 10  QTMSGAQIVASILKLEGIKQIIGFPNSELFDACAARD----IPPVIARTPRVAVNIAEGY 65

Query: 62  AR--ATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMV 119
           AR  A GE+ VV V  GPGA +A  GIA A+ D  P++ L         GY    E    
Sbjct: 66  ARTVADGELAVVTVQYGPGAESAFGGIAQAFNDRTPILFLP-------TGYPRGSEAVTP 118

Query: 120 GIS-----RPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDIL----NPAN 170
                   R V K S      E +P+++  A     +GRP PV+++LP D+L    +P N
Sbjct: 119 NFHASRNFRHVTKWSETAGCVEHLPKLMHSAISRVRNGRPAPVLLELPVDLLAERLDPTN 178

Query: 171 KLPYVWPESVSMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETV 230
           +        V  R       G  G+I   ++TL+AAK PVV  G G + A   ++L E  
Sbjct: 179 E--------VYQRPRRSAPQGDAGEIAELVKTLLAAKNPVVLAGQGVLAAFATKELVEFA 230

Query: 231 EALNLPVVCSLMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNN 290
           E L +PV+ +  G   FP  H  ALG  G       +  M  ADV+ A+G       +  
Sbjct: 231 ELLRIPVMTTPNGKSGFPENHPLALGAAGRARPTTVDHFMDKADVVLALGTSL--TRSYY 288

Query: 291 LAKYCPNATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLD--EIR 348
           +     +  +LH+ +D   + K       +V DAR  L QM   L Q   H  +D  ++ 
Sbjct: 289 ILPIPKDKVLLHVTVDEGDLGKDYPIAQGVVSDARSALRQMNAYLKQHK-HVLVDRADVM 347

Query: 349 DWWQQIEQ-WRARQCLKYDTHSEKIKPQAVI-ETLWRLTKGDAYVTSDVGQHQMFAALYY 406
           D  + I   +R R        SE I P  V+ E +  +   ++ VT D G  +   + +Y
Sbjct: 348 DEIRSIRSVFRERWMPLLTADSEPISPYRVVWEIMQVVDPSNSVVTHDAGNPRDQFSPFY 407

Query: 407 PFDKPRRWINSGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYEL 466
               PR +I  G    +G GL  ALG K+A P+ TVV + G+ +  M   +  TA++  L
Sbjct: 408 EAVIPRSYIGWGKTTQLGSGLGFALGAKLARPKATVVNLMGESAFGMVGIDFETAIRCHL 467

Query: 467 PVLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELES 526
           P+L V L N  LG        I S ++  + M     +  +AEA G  G  +S P  L  
Sbjct: 468 PILTVVLRNNVLGGYAASMP-IASRKYGANLMSGA--YAPIAEALGGYGECVSLPKNLRP 524

Query: 527 KLSEALEQVRNNRLVFVDV 545
            L   LE+V   +   ++V
Sbjct: 525 ALLRGLERVGKGQAALIEV 543


Lambda     K      H
   0.319    0.135    0.403 

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: 745
Number of extensions: 40
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: 574
Length of database: 555
Length adjustment: 36
Effective length of query: 538
Effective length of database: 519
Effective search space:   279222
Effective search space used:   279222
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 Jul 26 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