GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Desulfovibrio vulgaris Hildenborough

Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate 209328 DVU0392 aromatic aminotransferase

Query= BRENDA::Q9SIE1
         (475 letters)



>MicrobesOnline__882:209328
          Length = 399

 Score =  179 bits (454), Expect = 2e-49
 Identities = 127/397 (31%), Positives = 211/397 (53%), Gaps = 25/397 (6%)

Query: 72  LSPRVQSLKPSKTMVITDLAATLVQSGVPVIRLAAGEPDFDTPKVVAEAGINAIREGFT- 130
           +S RVQ ++ S T ++  LAA +       + L  G P F TP+ + EA   A+R+    
Sbjct: 7   VSRRVQQIRISATKLMPMLAARVGGC----VSLGQGVPSFRTPEHIVEAVCRALRDKADA 62

Query: 131 -RYTLNAGITELREAICRKLKEENGLSYAPD-QILVSNGAKQSLLQAVLAVCSPGDEVII 188
            RYTL  G+  LREAI   L    G    PD ++ V+ GA ++LL A+L V   GDEVII
Sbjct: 63  GRYTLQPGMPALREAIAADLAARKGYMVNPDSEVGVTVGAMEALLMALLTVVDRGDEVII 122

Query: 189 PAPYWVSYTEQARLADATPVVIPTKISNNFLLDPKDLESKLTEKSRLLILCSPSNPTGSV 248
           P+P + S+ EQ  +A+  PV +P + ++++ LD   + + +T ++R +I+C+P NPTG+V
Sbjct: 123 PSPGYASHAEQVLMAEGVPVHVPLR-ADDWGLDVDAIRAAVTPRTRAVIVCNPGNPTGTV 181

Query: 249 YPKSLLEEIARIIAKHPRLLVLSDEIYEHIIYAPATHTSFASLPDMYERTLTVNGFSKAF 308
           Y  + +  +  + A    ++++SDE Y++++Y      S ASLP+M    + VN FSK +
Sbjct: 182 YDDADVRALCEL-ALERNIMLISDETYDYMVYGGGEPLSPASLPEMRRHVIVVNSFSKKY 240

Query: 309 AMTGWRLGYLAGPKHIVAACSKLQGQVSSGASSIAQKAGVAALGLGKAGGETVAEMVKAY 368
           A+TGWR+GY A     +    K+    +  A +++Q A +AAL       + V +M  A 
Sbjct: 241 ALTGWRVGYCAADAAWMGELLKVHDAAAICAPAVSQYAALAAL---TGPQDCVDDMRAAL 297

Query: 369 RERRDFLVKSLGDI-KGVKISEPQGAFYLFIDFSAYYGSEAEGFGLINDSSSLALYFLDK 427
             RR+     L  +       +P+GAFY+    + Y  ++A        S  +A   L++
Sbjct: 298 SARRNLACARLDAMAPHFDYVQPRGAFYI---MARYTFTDA-------PSDMVARRLLEE 347

Query: 428 FQVAMVPGDAFG--DDSCIRISYATSLDVLQAAVEKI 462
            +V  VPG +FG   +  +R+S+      L  A +++
Sbjct: 348 GRVITVPGASFGPTGERHLRLSFGMEEAELDEAFDRM 384


Lambda     K      H
   0.317    0.132    0.370 

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: 396
Number of extensions: 22
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: 475
Length of database: 399
Length adjustment: 32
Effective length of query: 443
Effective length of database: 367
Effective search space:   162581
Effective search space used:   162581
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