GapMind for Amino acid biosynthesis

 

Alignments 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)



>MicrobesOnline__882:207383
          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.

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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