GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hcs in Desulfovibrio vulgaris Hildenborough

Align Putative homocitrate synthase AksA; EC 2.3.3.14; (R)-homo(2)citrate synthase; EC 2.3.3.-; (R)-homo(3)citrate synthase; EC 2.3.3.- (uncharacterized)
to candidate 207383 DVU1914 2-isopropylmalate synthase/homocitrate synthase family protein

Query= curated2:Q8TW28
         (397 letters)



>lcl|MicrobesOnline__882:207383 DVU1914 2-isopropylmalate
           synthase/homocitrate synthase family protein
          Length = 538

 Score =  169 bits (429), Expect = 1e-46
 Identities = 124/397 (31%), Positives = 197/397 (49%), Gaps = 23/397 (5%)

Query: 18  EVIVYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVSEGERDAVRRIAH 77
           ++ +YDTTLRDG Q+  ++     KL+IA  LDELG+  IE G+P  +  +    + I +
Sbjct: 4   QIHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKEIRN 63

Query: 78  EGLN-ADILCLARTLRGDVDAALDCDV--------DGVITFIATSELHLKHKLRMSREEV 128
             L  A I     T      A  D ++        D    F  + E H +  LR+     
Sbjct: 64  YNLKQAKISAFGSTHHPSHTAENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDGRRN 123

Query: 129 LERIADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRVHATDTVGVM 185
           L+ I D++ + K     V F AE   DG R    +   V R A E G D +   DT G  
Sbjct: 124 LDIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEVLRRAHEAGGDVLVLCDTNGGT 183

Query: 186 IPAAMRLFVAKIREVV-DLPIGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIGERAGN 244
           +P  +   V  +RE + +  +G+H H+D  +AVANS+AAV+AGA  +  T+NG+GER GN
Sbjct: 184 LPHEVHDIVTAVREQLPEAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGVGERCGN 243

Query: 245 AALEEVIMALK----ELYGIDPGFNTEVLAELSRKVSEYSGIDVPPNKAVVGENAFRHES 300
           A L  VI  L+      Y   P    + L  +S  VSE + +     +  VG +AF H+ 
Sbjct: 244 ANLSSVIPILELKSAGAYACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGRSAFAHKG 303

Query: 301 GIHVAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELG--VEPEEEIVEEV 358
           G+HV+AV      YE I P+ VG ++++++ +  GR  +V+     G  ++ +E +V+ +
Sbjct: 304 GVHVSAVNRNATLYEHITPESVGNHQRVLITELAGRSNIVSLARRFGFHLDKDEPVVKGL 363

Query: 359 LKRIK---ALGDRRVRVTDSKLEEIVRNVLESRGDRD 392
           +  +K   +LG       ++ +E ++   L  RG R+
Sbjct: 364 MNELKKKASLG-YDYAAAEASVELLLLRKLARRGVRE 399


Lambda     K      H
   0.317    0.135    0.380 

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: 455
Number of extensions: 19
Number of successful extensions: 5
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: 397
Length of database: 538
Length adjustment: 33
Effective length of query: 364
Effective length of database: 505
Effective search space:   183820
Effective search space used:   183820
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 (21.6 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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