GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Desulfovibrio vulgaris Hildenborough

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 208464 DVU2953 transcriptional regulator, GntR family

Query= BRENDA::A0A060PQX5
         (417 letters)



>lcl|MicrobesOnline__882:208464 DVU2953 transcriptional regulator,
           GntR family
          Length = 520

 Score =  220 bits (561), Expect = 7e-62
 Identities = 126/366 (34%), Positives = 195/366 (53%), Gaps = 7/366 (1%)

Query: 47  ISLAGGLPAPETFPVEIIAEITKEVLEKHAAQALQYGTTKGFTPLRLALAEWMRKRYDIP 106
           I+LA G      FP+       + VL +   +AL+Y    G+ PLR  +A  +  +  +P
Sbjct: 151 IALASGNSDARLFPLASFRRTLRTVLARDGIKALEYEDPAGYAPLRRTIARILADQ-GVP 209

Query: 107 ISKVDIMITSGSQQALDLIGRVFINPGDIVVVEAPTYLAALQAFKYYEPEFVQIPLDDEG 166
            +   +++T+GSQQAL L+ +V + PGD V VE P+Y   +  F+      V +  D EG
Sbjct: 210 ATPDTVLVTAGSQQALHLVAQVVLKPGDPVYVETPSYADGMALFRTLGLRIVPVFTDSEG 269

Query: 167 MRVDLLEEKLQELEKEGKKVKLVYTIPTFQNPAGVTMSEKRRKRLLELASEYDFLIVEDN 226
           M  + L E +    + G    LV+T+P FQNP G+ MS +RR+R+  +A  +   I+ED+
Sbjct: 270 MSAEGLREAIA---RHGHG--LVFTMPNFQNPTGICMSGQRRRRIAAIAVAHGVPILEDD 324

Query: 227 PYGELRYSGEPVKPIKAWDDEGRVMYLGTFSKILAPGFRIGWIAAEPHLIRKLEIAKQSV 286
             G++RY G     + +    G   Y GTFSK+L PG R+G++ AE  ++R L   K+  
Sbjct: 325 YVGDIRYEGYSQPSLHSLTPPGHTFYAGTFSKMLVPGLRMGYLVAEGPVLRMLARVKRMY 384

Query: 287 DLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFYKPRRDAMLKALEEFMPEGVRWTKPEGGM 346
           DL T+   Q    ++V+ G    H+      YK RRDA+L +    +P+ V      GG+
Sbjct: 385 DLSTSSVVQRTLERFVDLGSYRAHLTRACRIYKVRRDALLDSAVRHLPDDVTIAPVRGGL 444

Query: 347 FVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAFFAH-RDVKNTMRLNFTYVPEEKIREGIK 405
           F W+TLPEG+   ++  +A   GV   PG  FFA   + +  +R+NFT    E + EG++
Sbjct: 445 FAWMTLPEGVGATVLAHEAARHGVTVTPGTPFFAEGLEGERHLRINFTQHDPEILEEGMR 504

Query: 406 RLAETI 411
           RLA  I
Sbjct: 505 RLARAI 510


Lambda     K      H
   0.318    0.137    0.398 

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: 516
Number of extensions: 36
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: 417
Length of database: 520
Length adjustment: 33
Effective length of query: 384
Effective length of database: 487
Effective search space:   187008
Effective search space used:   187008
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: 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 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