GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hcs in Synechococcus elongatus PCC 7942

Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate Synpcc7942_1410 Synpcc7942_1410 2-isopropylmalate synthase

Query= BRENDA::D0VY45
         (540 letters)



>FitnessBrowser__SynE:Synpcc7942_1410
          Length = 540

 Score =  454 bits (1168), Expect = e-132
 Identities = 258/522 (49%), Positives = 339/522 (64%), Gaps = 23/522 (4%)

Query: 25  VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84
           + I DTTLRDGEQSPGA++   +KL  ARQLA+L VDIIEAGF  AS  DF AV+ IA E
Sbjct: 10  ILIFDTTLRDGEQSPGASLNLEEKLAIARQLARLNVDIIEAGFAFASPGDFEAVQRIAAE 69

Query: 85  VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144
           VG   DG    P I  ++R   +DI  A EAL  A + R+ TFIATS IH+EYKL+K++ 
Sbjct: 70  VGT-PDG----PTICSLARATRQDIKAAAEALAPAAKGRIHTFIATSDIHLEYKLKKTRA 124

Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204
           +VL     MV +A SL   D++F  EDA RSD EFLY+     I AGA T+ IPDTVG  
Sbjct: 125 EVLAVIPEMVGYAASL-VDDVEFSPEDAGRSDPEFLYECLEAAIAAGAKTINIPDTVGYT 183

Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264
            P E+G LI  IK N   I+ AI++ H HNDLGLA AN +E  + GARQLE TINGIGER
Sbjct: 184 TPSEFGALIGGIKQNVCNIDQAIISVHGHNDLGLAVANFLEAVKNGARQLECTINGIGER 243

Query: 265 AGNASFEEVVMALTC----------RGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQP 314
           AGNA+ EE+VMAL            R  D    L T +NTR I KTS++V   +G+ +QP
Sbjct: 244 AGNAALEELVMALHVRRQYFNPFLGRAADSEAPL-TQVNTREIYKTSRLVSNLTGMLVQP 302

Query: 315 HKALVGANAFLHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNR 374
           +KA+VGANAF HESGIHQDG+LK++ TYEI+  E IGL     + I LGKLSGR A R R
Sbjct: 303 NKAIVGANAFAHESGIHQDGVLKNKLTYEIVDAETIGLST---NRITLGKLSGRNAFRTR 359

Query: 375 LEELGYKLKDTEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCG 434
           L+ELGY L + ++   F +FK +A+KK+ +TD DL A+V++E      ++KL  +QV+ G
Sbjct: 360 LQELGYDLGEDDLNRAFLRFKELADKKREVTDRDLEAIVNDETQQAPELFKLELVQVSAG 419

Query: 435 TVGFSTATVKLFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDA 494
                TATV L + +G      +IGTGPVD+ Y+AIN +V  P +L+++++ ++T GIDA
Sbjct: 420 DHARPTATVTLRTPEGEELTDAAIGTGPVDAIYRAINRVVNIPNELIEFSVKSVTAGIDA 479

Query: 495 TATTSVEISRGDTNHPVFSGTGGGTDVVVSSVDAYLSALNNM 536
               ++ +   D    +FSG    TD++V+S  AY+ ALN +
Sbjct: 480 IGEVTIRLRHEDR---IFSGHSANTDILVASAQAYIHALNRL 518


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: 612
Number of extensions: 19
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: 540
Length adjustment: 35
Effective length of query: 505
Effective length of database: 505
Effective search space:   255025
Effective search space used:   255025
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