GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Pseudomonas fluorescens GW456-L13

Align Probable 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate PfGW456L13_3378 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)

Query= curated2:O27439
         (419 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378
          Length = 866

 Score =  105 bits (262), Expect = 5e-27
 Identities = 110/458 (24%), Positives = 197/458 (43%), Gaps = 69/458 (15%)

Query: 4   TVSEKILARASGKDRVEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKIVVI 63
           T+++K++ +A G   V  G      +    + D TGP++ +  + +     +  + ++  
Sbjct: 383 TLAQKMVGKACGVTGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLA-CLGFSTDLVMQS 441

Query: 64  FDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVGTDS 123
           F H            H  + DF+  +G  +     +G+ H  L     ++P  V  G DS
Sbjct: 442 FCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRP-GDGIIHSWLNRM--LLPDTVGTGGDS 498

Query: 124 HTCTHGALGAFATGI----GSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKDVI- 178
           HT        F  GI    GS  +A   ATG +   +PE++    +G+L+  V  +D++ 
Sbjct: 499 HT-------RFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGELQPGVTLRDLVH 551

Query: 179 ----------LNIIGRVGADGATYMACEFAG-----ETVAEMSVSDRMVLSNMAIEMGG- 222
                     L  + + G   A      F+G     E + +++V     LS+ + E    
Sbjct: 552 AIPYYAIQAGLLTVEKKGKKNA------FSGRILEIEGLPKLTVEQAFELSDASAERSAA 605

Query: 223 -------KTGIVEPDEKTLNYVRRRSGKPW--------------------RVFKTDPDAP 255
                  K  I E  +  +  +R   G+ +                     + + D DA 
Sbjct: 606 GCTIQLSKESIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLANPELLEADKDAE 665

Query: 256 SLSVMEVDVSDLEPQVAC-PHNVDNVKPVTEVEGTEIDQVFLGSCTNGRLSDLRDAAAIL 314
              V+E+D++D++  V C P++ D+ + ++ V G +ID+VF+GSC    +   R A  +L
Sbjct: 666 YAEVIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMT-NIGHFRAAGKLL 724

Query: 315 KNRKVSDSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPCLGGHVGLVGPGE 374
           +  K     R+ + P ++    +  +EG   I+  AGA +  P C  C+G     V P  
Sbjct: 725 EQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQ-ARVEPNS 783

Query: 375 VSLSTSNRNFRGRQGSPEAEVYLSSAAVAAASAVKGSI 412
             +STS RNF  R G   A VYL+SA +A+ +++ G +
Sbjct: 784 TVVSTSTRNFPNRLGD-GANVYLASAELASVASILGRL 820


Lambda     K      H
   0.318    0.135    0.396 

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: 817
Number of extensions: 42
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 419
Length of database: 866
Length adjustment: 37
Effective length of query: 382
Effective length of database: 829
Effective search space:   316678
Effective search space used:   316678
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