GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ARO8 in Pseudomonas fluorescens GW456-L13

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate PfGW456L13_4175 Transcriptional regulator, GntR family domain / Aspartate aminotransferase (EC 2.6.1.1)

Query= SwissProt::H3ZPL1
         (417 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4175
          Length = 388

 Score =  242 bits (618), Expect = 1e-68
 Identities = 142/392 (36%), Positives = 212/392 (54%), Gaps = 15/392 (3%)

Query: 22  FSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITKEVLEKHAAQALQ 81
           FSE+   +K+S IRE+L   +   V+S AGGLPA    P        K    +      Q
Sbjct: 3   FSERVSRLKSSLIREILAAAQRPQVMSFAGGLPAETMLP--------KVEWAEMPVSMGQ 54

Query: 82  YGTTKGFTPLRLALAEWMRERYDIPISKVDIMTTSGSQQALDLIGRVFINPGDIIVVEAP 141
           YG ++G   LR ALA   R    +P     ++  SGSQQ LDL  +++I+ G  I++EAP
Sbjct: 55  YGMSEGEPALREALAAEARA-LGVPCEASQVLVVSGSQQTLDLAAKLYIDKGTEILLEAP 113

Query: 142 TYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKVKIVYTIPTFQNPAGV 201
           TYLAALQ F+ +  + + + L+ +G N+  L  +L++      +   +Y IPTFQNP+ V
Sbjct: 114 TYLAALQIFQLFGADCLTVSLEADGPNLTALRARLEQ-----HRPAFIYLIPTFQNPSAV 168

Query: 202 TMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDEEGRVIYLGTFSKILA 261
             +E +R  +  L  ++   ++ED PY EL + G    PI +  +    IY GT SK L 
Sbjct: 169 RYSEAKRNAVAALLDEFGVTLIEDEPYRELTFDGGCATPIVSRLKRASWIYTGTVSKTLL 228

Query: 262 PGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGYLDKHIPKIIEFYKPR 321
           PG R+G++ A P     L   KQS DL TN   Q  A +++      +H  ++ +FY+ R
Sbjct: 229 PGLRVGYLIASPDLFPHLLKLKQSADLHTNRVGQWQALQWIGTEKYQQHRSELRDFYRGR 288

Query: 322 RDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAVAKGVAYVPGEAFFAH 381
           RDA   ALE    D   W  P+GG+F W  L +  DT+ +L  A+A  VA++PGE FF  
Sbjct: 289 RDAFQAALETHFSDLADWNVPQGGLFFWLKLKQPQDTRTLLNAALANDVAFMPGEPFFPE 348

Query: 382 RD-VKNTMRLNFTYVPEEKIREGIKRLAETIK 412
            D     +RLNF+++   ++ EG+KRLA  ++
Sbjct: 349 PDNHPGYLRLNFSHIDPARLDEGLKRLAAVVR 380


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: 400
Number of extensions: 17
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: 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 Sep 17 2021. The underlying query database was built on Sep 17 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