GapMind for Amino acid biosynthesis

 

Alignments 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)



>MicrobesOnline__882:208464
          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 (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