GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Pseudomonas fluorescens FW300-N2C3

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate AO356_19495 AO356_19495 GntR family transcriptional regulator

Query= BRENDA::A0A060PQX5
         (417 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_19495
          Length = 388

 Score =  243 bits (621), Expect = 6e-69
 Identities = 142/398 (35%), Positives = 220/398 (55%), Gaps = 21/398 (5%)

Query: 22  FSKKALGMKASEVRELLKLVESSDVISLAGGLPAPETFPVEIIAEITKEVLEKHAAQAL- 80
           FS++   +K+S +RE+L   +  +V+S AGGLPA    P             + AA  L 
Sbjct: 3   FSERVSRLKSSLIREILAAAQRPEVMSFAGGLPAEAMLPKV-----------EWAAMPLS 51

Query: 81  --QYGTTKGFTPLRLALAEWMRKRYDIPISKVDIMITSGSQQALDLIGRVFINPGDIVVV 138
             QYG ++G   LR ALA   R    +      +++ SGSQQ LDL  ++ I+ G  V++
Sbjct: 52  MGQYGMSEGEPALREALAAQARG-LGVACEASQVLVVSGSQQTLDLAAKLHIDVGTEVML 110

Query: 139 EAPTYLAALQAFKYYEPEFVQIPLDDEGMRVDLLEEKLQELEKEGKKVKLVYTIPTFQNP 198
           EAPTYLAALQ F+ +  + + +PL+ +G  +  L  +L++      +   +Y IPTFQNP
Sbjct: 111 EAPTYLAALQIFQLFGADCITVPLEADGPDLHQLRARLEQ-----HRPAFIYLIPTFQNP 165

Query: 199 AGVTMSEKRRKRLLELASEYDFLIVEDNPYGELRYSGEPVKPIKAWDDEGRVMYLGTFSK 258
           + V  SE +R  +  L  E+   ++ED PY EL + G    PI +   +   +Y GT SK
Sbjct: 166 SAVRYSEAKRDAVAALLDEFGVTLIEDEPYRELTFDGGSATPIVSRLKKASWIYTGTVSK 225

Query: 259 ILAPGFRIGWIAAEPHLIRKLEIAKQSVDLCTNPFSQVIAWKYVEGGHLDNHIPNIIEFY 318
            L PG R+G++ A P L   L   KQS DL TN   Q  A +++      +H+  + +FY
Sbjct: 226 TLLPGLRVGYLIASPDLFPHLLRLKQSADLHTNRIGQWQALQWIGTEQYRSHLSELRDFY 285

Query: 319 KPRRDAMLKALEEFMPEGVRWTKPEGGMFVWVTLPEGIDTKLMLEKAVAKGVAYVPGEAF 378
           + RRD    AL++   +   W  P+GG+F W+TL + +DT+ +L  A+A  VA++PGE F
Sbjct: 286 RDRRDRFQAALQKHFSDIADWNVPQGGLFFWLTLRQPLDTRTLLAAALAADVAFMPGEPF 345

Query: 379 FAHRDV-KNTMRLNFTYVPEEKIREGIKRLAETIKEEM 415
           F   D     +RLNF+++   ++ EG+KRLA  ++E +
Sbjct: 346 FPEPDQHPGHLRLNFSHIDPARLDEGLKRLAGVVREAL 383


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: 404
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: 417
Length of database: 388
Length adjustment: 31
Effective length of query: 386
Effective length of database: 357
Effective search space:   137802
Effective search space used:   137802
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: 50 (23.9 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