GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Dyella japonica UNC79MFTsu3.2

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate N515DRAFT_1567 N515DRAFT_1567 pyruvate dehydrogenase (quinone)

Query= BRENDA::P9WG41
         (618 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1567
          Length = 594

 Score =  216 bits (549), Expect = 3e-60
 Identities = 168/556 (30%), Positives = 260/556 (46%), Gaps = 43/556 (7%)

Query: 44  VIRSLEELGVDVIFGIPGGAVLPVYDPLFDS-KKLRHVLVRHEQGAGHAASGYAHVTGRV 102
           ++  L + G+  +FG PG  +  +   +  + ++  +V VRHE+ A   A G+A  TGR+
Sbjct: 8   ILERLSDWGIQRVFGYPGDGINGLMGAMGRAAERFDYVRVRHEEMAAFMACGHAKFTGRI 67

Query: 103 GVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITMPITKH 162
           GVC+ATSGPGA +L+  L DA++D +PV+AI GQ  R  +G+D  QE D+  +   +  +
Sbjct: 68  GVCLATSGPGAIHLLNGLYDARLDHMPVLAIVGQQARAALGSDYQQEVDLQALFKDVANY 127

Query: 163 NFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRMELPGYK---- 218
              V +   +  VL  A  IA + R   V++ +P D LQ       PPR     Y     
Sbjct: 128 AQTVTTPAQVRHVLDRAIRIAQAERAVTVVI-VPHD-LQLMPAVPSPPRKHGNVYSGVGL 185

Query: 219 --PNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLMAR 276
             P+ +P + ++  AA +I A+ +  + VG G +  +A+ ++R+LAE     V   L+ +
Sbjct: 186 ALPHPQPTAMELERAASVINASERVAILVGAGAL--DASTEVRQLAERLDAGVAKALLGK 243

Query: 277 GAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAP---EAKVI 333
              PD      G  G+ G+  +   +   D L+ +GT F          F P   +A+ +
Sbjct: 244 TVLPDDLPYVTGPIGLLGSKPSWRLMNGCDTLLMIGTTF------PYSEFLPPDGQARAV 297

Query: 334 HADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPG-----TIEMADWWAYLNGV 388
             DI P  +     A+V +VGD    I  L+ +L             +++  WW  L G 
Sbjct: 298 QIDIAPRNMSLRYPAEVNLVGDAAQTIRRLLPLLSEKRNADWRERIEVDVRKWWRLLEG- 356

Query: 389 RKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLN 448
           R   P S        ++P+ V  +L +     A+     G H  W A+ ++  +      
Sbjct: 357 RAMAPAS-------PINPQRVFWELSDCLPDRAIVCGDCGSHTGWFARDVKLREGMLASL 409

Query: 449 SGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMT-NQELATCAV-----EGIPVKV 502
           SGGL TMG  +P A+ AK+A P   V AI GDG  QM  N EL T              V
Sbjct: 410 SGGLATMGGGVPYAIAAKMAWPDRPVLAIVGDGAMQMNGNAELVTVKQYWRRWSDPRFVV 469

Query: 503 ALINNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVD 562
            +++N +L  V   Q     +   + D A      P + + AE LG  GLR +R E + D
Sbjct: 470 LVVSNRDLNQVTWEQRALAGD--PKFDAAQDVEPFP-YARYAELLGFRGLRVDRPEQITD 526

Query: 563 VINQARAINDCPVVID 578
              QA A  DCPVVI+
Sbjct: 527 AWRQAFAA-DCPVVIE 541


Lambda     K      H
   0.319    0.136    0.414 

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: 897
Number of extensions: 44
Number of successful extensions: 4
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: 618
Length of database: 594
Length adjustment: 37
Effective length of query: 581
Effective length of database: 557
Effective search space:   323617
Effective search space used:   323617
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: 53 (25.0 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