GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hcs in Klebsiella michiganensis M5al

Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate BWI76_RS04680 BWI76_RS04680 2-isopropylmalate synthase

Query= BRENDA::D0VY45
         (540 letters)



>FitnessBrowser__Koxy:BWI76_RS04680
          Length = 523

 Score =  363 bits (931), Expect = e-104
 Identities = 219/515 (42%), Positives = 311/515 (60%), Gaps = 19/515 (3%)

Query: 25  VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84
           V I DTTLRDGEQ+  A+++  +KL+ A  L ++GVD++E GFP +S  DF +V+ IA  
Sbjct: 5   VIIFDTTLRDGEQALQASLSVKEKLQIAMALERMGVDVMEVGFPVSSPGDFESVQTIART 64

Query: 85  VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144
           + N          +  ++RC EKDI  A E+LK A+  R+ TFIATSP+H+  KLR + D
Sbjct: 65  IKNSR--------VCALARCVEKDIDVAAESLKVAEAFRIHTFIATSPMHIATKLRSNLD 116

Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204
           +V+E A  MVK AR+    D++F  EDA R+    L ++    I AGATT+ IPDTVG  
Sbjct: 117 EVIERAIYMVKRARNY-TDDVEFSCEDAGRTPIADLARVVEAAINAGATTINIPDTVGYT 175

Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264
           MPFE+  +I  +  + P I+ AI++ H H+DLG+A  N +     GARQ+E  +NGIGER
Sbjct: 176 MPFEFANIITGLYEHVPNIDKAIISVHTHDDLGIAVGNALAAVHAGARQVEGAMNGIGER 235

Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324
           AGN S EEV+MA+  R  DI+  +HT IN + I +TS+ V +   + +  +KA+VG  AF
Sbjct: 236 AGNCSLEEVIMAIKVRK-DIM-NVHTRINHQEIWRTSQTVSQICNMPIPANKAIVGTGAF 293

Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384
            H SGIHQDG+LK+R  YEI++PE IGL +     + L   SGR A+++R+EE+GYK  D
Sbjct: 294 AHSSGIHQDGVLKNRENYEIMTPESIGLNQV---QLNLTSRSGRAAVKHRMEEMGYKETD 350

Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQP-IWKLGDLQVTCGTVGFSTATV 443
             ++ ++  F  +A+KK ++ D DL AL       E+P  ++L    V  G+   +TA+V
Sbjct: 351 YNMDHLYDAFLKLADKKGQVFDYDLEALAFINKQQEEPEHFRLDYFSVQSGSSDIATASV 410

Query: 444 KLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEIS 503
           KL   D +   A + G GPVD+ Y+AIN I     +LVKY L A  +G DA     +   
Sbjct: 411 KLACGDETKAEAAN-GNGPVDAIYQAINRITGYEIELVKYDLNAKGQGKDALGQVDIV-- 467

Query: 504 RGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNMLR 538
             + N   F G G  TD+V SS  A +  LNN+ R
Sbjct: 468 -ANYNGRRFHGVGLATDIVESSAKAMVHVLNNIWR 501


Lambda     K      H
   0.318    0.134    0.390 

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: 601
Number of extensions: 26
Number of successful extensions: 6
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: 540
Length of database: 523
Length adjustment: 35
Effective length of query: 505
Effective length of database: 488
Effective search space:   246440
Effective search space used:   246440
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.

Links

Downloads

Related tools

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