GapMind for Amino acid biosynthesis

 

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

Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate Pf1N1B4_3888 Aconitate hydratase (EC 4.2.1.3)

Query= curated2:Q9WYC7
         (418 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888
          Length = 913

 Score = 96.3 bits (238), Expect = 3e-24
 Identities = 119/493 (24%), Positives = 198/493 (40%), Gaps = 115/493 (23%)

Query: 25  LARVDIAMAQDGTGPLMINEFRELGFKEVKVPKAFLFIDHASPSP-------RKELSNSQ 77
           LA +  AMA+ G  P  IN    +   ++ +  + +   +AS S          + ++ +
Sbjct: 100 LAAMRAAMAKAGGDPQRINPLSPV---DLVIDHSVMVDKYASASAFGQNVDIEMQRNHER 156

Query: 78  KMMREFGKEM--GVKVFDAGDGISHQILAE--------------KYVKPGDLVAGADSHT 121
                +G+       V   G GI HQ+  E               Y  P  LV G DSHT
Sbjct: 157 YAFLRWGQSAFNNFSVVPPGTGICHQVNLEYLGRTVWTKDEDGRTYAFPDTLV-GTDSHT 215

Query: 122 CTAGGLGAFGTGMGSTDVAIIFGLGQNW-FKVPETIKVVVNGKLQDGVYAKDIILEIARI 180
               GLG  G G+G  +      LGQ     +PE I   + GKL++G+ A D++L + ++
Sbjct: 216 TMINGLGVLGWGVGGIEAEAAM-LGQPVSMLIPEVIGFKLTGKLKEGITATDLVLTVTQM 274

Query: 181 LGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFLKKMGREE 240
           L   G   K +EF+G  + ++ + DR TI+NMA E GA  G  P DE T E+L+  GR  
Sbjct: 275 LRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYGATCGFFPVDEVTLEYLRLSGRTP 334

Query: 241 DFREL------------KADPDAVYETEIEIDATTLE----------PLVSLPH------ 272
              +L                + V+   + +D  ++E            VSLP+      
Sbjct: 335 QTVKLVEAYSKTQGLWRLPGKEPVFTDSLALDMGSVEASLAGPKRPQDRVSLPNVAQAFT 394

Query: 273 -YVDNVRKVSEVEKEKIKID---QVFIGTC------------TNGRLQDLEIALKILEK- 315
            ++    K S  E+ +++ +    V +G              +  RL++  + +  +   
Sbjct: 395 DFLGLQFKPSSKEEGRLESEGGGGVAVGNADLIGEADYHHEGSTYRLKNGAVVIAAITSC 454

Query: 316 -HGKHPDVRLIVGPASRKVYMDALEKGIIKK--------------------------FVE 348
            +  +P V +  G  ++K    A+EKG+ +K                            E
Sbjct: 455 TNTSNPSVMMAAGLVAKK----AVEKGLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDE 510

Query: 349 LGAAVIPPGCGPCVGIHMGVLGDGERVLS----------TQNRNFKGRMGNPNAEIYLAS 398
           LG A++  GC  C+G    +    E+ +           + NRNF+GR+       +LAS
Sbjct: 511 LGFALVGYGCTTCIGNSGPLPEPIEKAIQKADLTVASVLSGNRNFEGRVHPLVKTNWLAS 570

Query: 399 PATAAATAVTGYI 411
           P    A A+ G +
Sbjct: 571 PPLVVAYALAGTV 583


Lambda     K      H
   0.318    0.137    0.395 

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: 790
Number of extensions: 42
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 418
Length of database: 913
Length adjustment: 37
Effective length of query: 381
Effective length of database: 876
Effective search space:   333756
Effective search space used:   333756
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: 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