GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Pseudomonas fluorescens FW300-N1B4

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Pf1N1B4_696 Acetolactate synthase, large subunit (EC 2.2.1.6)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_696
          Length = 545

 Score =  220 bits (560), Expect = 1e-61
 Identities = 168/559 (30%), Positives = 264/559 (47%), Gaps = 37/559 (6%)

Query: 3   MLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLA 62
           M +  E++V+ L D GV+QVFG PG   +++Y  L     I+HV  RHEQ A  MADG A
Sbjct: 1   MATCGEVLVKLLEDYGVEQVFGIPGVHTVELYRGLAR-SSINHVTPRHEQGAGFMADGYA 59

Query: 63  RATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIG------YDAFQEC 116
           R +G+ GV  + +GPG TN  T +  AY DSIP++V+S   + S +G      ++   + 
Sbjct: 60  RTSGKPGVCFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRSQLGGGRGKLHELPNQS 119

Query: 117 DMVGISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDIL-NPANKLPYV 175
            +VG    V   S  +    ++P VL +AF L  +GRP PV +++P D+L   A+ L   
Sbjct: 120 ALVG---GVAAFSHTLMSAAELPGVLARAFALFQAGRPRPVHIEIPLDVLVEEADDLLAS 176

Query: 176 WPESVSMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNL 235
            P ++     +P+       I R    L  AK+P++  GGGAI A    +L E  E L+ 
Sbjct: 177 VPVNIDRAGASPSA------ISRMTDWLAGAKRPLILAGGGAIDAAA--ELTELAELLDA 228

Query: 236 PVVCSLMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRF--DDRTTNNLAK 293
           PV  ++   G   + H   +G             +  ADV+ A+G      D        
Sbjct: 229 PVALTINAKGMLESRHPLLIG--STQSLVATRALVAEADVVLAIGTELAETDYDITFAGG 286

Query: 294 YCPNATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQ 353
           +     +L +DIDP    +     + +V D+R   + +L  LS    H+ L E R+ W Q
Sbjct: 287 FEIPGVLLRVDIDPDQTVRNYPPKVALVADSRNAAQALLSALS----HKSLAERRNDWGQ 342

Query: 354 IEQWRARQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRR 413
           +     R  L     +  +     +ET+        +V  D  Q      L +  ++PRR
Sbjct: 343 VRAAHLRDELAASWDAPTLAQTRFLETVLHELPNAVFV-GDSTQPVYTGNLTFNPERPRR 401

Query: 414 WINSG-GLGTMGFGLPAALGVKMALPEE-----TVVCVTGDGSIQMNIQELSTALQYELP 467
           W NS  G GT+G+ LPAA+G  +    E      VVC+ GDG +Q  + EL++A++   P
Sbjct: 402 WFNSSTGYGTLGYALPAAIGAWLGGRVEGGARPPVVCLIGDGGLQFTLPELASAVEARTP 461

Query: 468 VLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESK 527
           V+V+  NN+    +K++  M+             PDF+ +A+A G     +S    L   
Sbjct: 462 VIVLLWNNQGYEEIKKY--MVNRAIEPVGVDIYTPDFIGVAKALGCAAEAVSSVDGLRDA 519

Query: 528 LSEALEQVRNNRLVFVDVT 546
           L  A ++ +   L+ +D T
Sbjct: 520 LRLATDR-QGPTLIEIDQT 537


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: 776
Number of extensions: 44
Number of successful extensions: 8
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: 545
Length adjustment: 36
Effective length of query: 538
Effective length of database: 509
Effective search space:   273842
Effective search space used:   273842
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:

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