GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Burkholderia phytofirmans PsJN

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate BPHYT_RS23060 BPHYT_RS23060 3-isopropylmalate dehydratase large subunit

Query= curated2:B2KBD7
         (418 letters)



>FitnessBrowser__BFirm:BPHYT_RS23060
          Length = 655

 Score =  202 bits (513), Expect = 3e-56
 Identities = 150/444 (33%), Positives = 223/444 (50%), Gaps = 38/444 (8%)

Query: 2   PQTIAEKIISNH---SGRRVKAGEFVIADVDLTAVQDGTGPLTVEELKKAGFTK---LAN 55
           P+T+ EKII  H   +    + G+ V    D     D    +    + +A F K   L  
Sbjct: 206 PKTLVEKIIERHLHPASVGAQRGDGVFIAADWRFSHDYFTGMCAHLMHRA-FGKPAPLHA 264

Query: 56  PARTILFIDH------AAPSPRKEL----SNSQVVLRNFAKET-----GAILSEIG-EGV 99
           P   I F DH      + P  R  L    +N      +F+++      GA+    G EG+
Sbjct: 265 PDHIIAFQDHLVLASQSIPHVRDGLLPGVANLMEGHTSFSRDYPVRSHGALDGMPGSEGI 324

Query: 100 CHQLLAEKYVNPGEILIGADSHTCTGGALGAFATGMGSTDVAVGMALGKTWLKAPQTFKI 159
           CH L+AE+Y  PG++  G DSHT   GALG  A G G+T++A     G    K P+T +I
Sbjct: 325 CHALMAEQYALPGQVACGTDSHTPHSGALGCLAFGAGATEIANSWVTGYVRCKVPETLRI 384

Query: 160 EVEGAFKKGVGAKDLILHLI--GVIGADGATYKALEFHGSTIRNMEMADRFTLANMAVEA 217
           E+ G  + GV AKD++LHL+    I + GA     E+ GS +R M + +R TL NM  E 
Sbjct: 385 EISGQLRDGVTAKDVVLHLLQMDAIRSGGAIGLVFEYGGSAVRAMSIDERATLTNMVAEL 444

Query: 218 GAKAGLFFTDEKTRAYLAERGRGDNFKL---ISADEGADYEKVIKIDASSLEPTVSCPHT 274
           G   G+   DE+T A+L ER RG +F L   + +D GA Y   I IDAS+++P ++ P  
Sbjct: 445 GGFTGIVEPDERTVAFLKER-RGVDFTLENWMKSDAGATYRDTISIDASAIQPMLARPGD 503

Query: 275 VDNTKTVGEL-KDIKVNQVFIGTCTNGRIEDLRIAAEIL-----KDKKVNPGTRTFITPA 328
             N     +L +D+ ++  + G+CT G+ ED     E+L     +  +V  GTR ++   
Sbjct: 504 PGNGVPALQLEQDVAIDIAYGGSCTAGKREDFDFYHEVLHWGVEQGLRVPEGTRLYLQFG 563

Query: 329 SRDVMLAALKEGLIEIFVKAGASVQTPGCGPCVGVHGGILGD-GEVCLATQNRNFQGRMG 387
           +  V     + G + +F +AG ++  PGCG C     G   +  EV ++  NRNF GR G
Sbjct: 564 TMAVRAYCEERGYLPVFERAGVTLVMPGCGSCANCGPGQSAEANEVTISAINRNFPGRSG 623

Query: 388 NTKGFIYLSSPAVAAYSALKGYIS 411
              G ++L+SP   A SAL G I+
Sbjct: 624 --PGNVWLASPYTVAASALAGKIT 645


Lambda     K      H
   0.317    0.135    0.388 

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: 619
Number of extensions: 32
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 418
Length of database: 655
Length adjustment: 35
Effective length of query: 383
Effective length of database: 620
Effective search space:   237460
Effective search space used:   237460
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: 52 (24.6 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