GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Caulobacter crescentus NA1000

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate CCNA_00196 CCNA_00196 3-isopropylmalate dehydratase large subunit

Query= curated2:O27668
         (428 letters)



>FitnessBrowser__Caulo:CCNA_00196
          Length = 479

 Score =  202 bits (514), Expect = 2e-56
 Identities = 148/447 (33%), Positives = 213/447 (47%), Gaps = 69/447 (15%)

Query: 30  VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPANTIGAAEFQRVTRE 89
           +DL + H+ T+P   + F  + + G   R   P+R + V DHN+P     A     V  E
Sbjct: 27  IDLHLIHEVTTP---QAFAGLRAAGRKVR--RPDRTLAVADHNIPTEG-QALGVDAVADE 80

Query: 90  FAREQGIVNIFQNAA--------------GICHQVLPERGFVRPGMVIVGADSHTCTYGA 135
            AR Q +  + +N A              GI H V PE+G  +PGM IV  DSHT T+GA
Sbjct: 81  EARLQ-LKTLARNVADNGIEFFPMGDIRNGIVHVVGPEQGRTQPGMTIVCGDSHTSTHGA 139

Query: 136 FGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGA 195
           FGA A G+G +++  V AT        + M + V G+    V  KDV L +IGEIG  G 
Sbjct: 140 FGALAHGIGTSEVEHVLATQTLRQKKAKNMLVRVDGQLPPGVTGKDVALAVIGEIGTAGG 199

Query: 196 TYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRARTG-------- 247
           T   +EF G+ I  + + GRMT+CN+ +E GAK G++ P+ +T  Y++ +          
Sbjct: 200 TGYVIEFAGEAIAGLSMEGRMTLCNLTIEGGAKAGLVAPDDKTFAYIQGKPAAPKGAAWD 259

Query: 248 ---REFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPV---------------- 288
                ++ + +DED+ +      D S L P V      ++V PV                
Sbjct: 260 MALSHWKTFFTDEDAVFDRTVVIDGSALVPMVTWGTSPEDVIPVTGNVPDPESFATPDKR 319

Query: 289 ---HR------------VEGTHIDEAFLGSCTNGRYEDLKIAAEVIGD-----RRVHEDV 328
              HR            +    ID  F+GSCTN R ED++ AA V+ +     R V   V
Sbjct: 320 AAAHRALDYMGLKAGQPISEARIDRVFIGSCTNSRIEDMRAAAAVVQEAFLHGRLVAPHV 379

Query: 329 RFIVSPASREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRN 388
           + +V P S  +  +A E+G+   F  AG     PGC  CL  +   LAP E   +T+NRN
Sbjct: 380 KAMVVPGSGLVKEQAEEEGLDAIFKAAGFDWREPGCSMCLAMNPDKLAPQERCASTSNRN 439

Query: 389 FRGRMGDPASSVYLANPAVVAESAIEG 415
           F GR G  A   +L +PA+ A +AI G
Sbjct: 440 FEGRQG-RAGRTHLVSPAMAAAAAIAG 465



 Score = 24.3 bits (51), Expect = 0.009
 Identities = 17/54 (31%), Positives = 26/54 (48%)

Query: 371 HMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAPQQEA 424
           +MG+ A   +S A  +R F G   +       A  AVV E+ + G + AP  +A
Sbjct: 328 YMGLKAGQPISEARIDRVFIGSCTNSRIEDMRAAAAVVQEAFLHGRLVAPHVKA 381


Lambda     K      H
   0.320    0.137    0.408 

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: 577
Number of extensions: 39
Number of successful extensions: 6
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: 428
Length of database: 479
Length adjustment: 33
Effective length of query: 395
Effective length of database: 446
Effective search space:   176170
Effective search space used:   176170
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: 51 (24.3 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