GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruH in Pseudomonas fluorescens FW300-N1B4

Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Pf1N1B4_4425 Aspartate aminotransferase (EC 2.6.1.1)

Query= BRENDA::Q9HUI9
         (393 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4425
          Length = 403

 Score =  187 bits (475), Expect = 5e-52
 Identities = 133/404 (32%), Positives = 197/404 (48%), Gaps = 16/404 (3%)

Query: 1   MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60
           +R S   QR++    AA     +A A  E G +IL L++G+PDFDTP  I QAA  ++  
Sbjct: 3   VRLSKRVQRVSLSANAA--AKSQATALREAGRDILDLTIGEPDFDTPEHIKQAAYAAIAG 60

Query: 61  GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120
           G T Y    G +ALR  +  + R+ +      E +V+  GA+  ++      L+ GD+V+
Sbjct: 61  GATKYTPTPGVKALRIAVQRKLRQENHLDYPLESIVIANGAKQIIFNAFAATLDDGDQVL 120

Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180
           V  P + ++       G   V +      G ++ AE++   I  RTR + LN P NPSGA
Sbjct: 121 VPTPYWPSFPDSVRFNGGEPVFIECGLAQGCKLTAEQLEQYIGERTRWLILNGPGNPSGA 180

Query: 181 SLPRATWEALAELCMAH-DLWMISDEVYSELLFDGEHVSP--ASLPGMADRTATLNSLSK 237
               A  +ALAE+   H  + ++ DE+Y  + FDG       +  P +  R   +  +SK
Sbjct: 181 VYSAAELQALAEVLRRHPQVLILLDELYEHIRFDGRPAQSLLSVAPDLQSRCLLVGGVSK 240

Query: 238 SHAMTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYR 297
           ++AMTGWR+G+  GP AL   +  +      G+    Q AA  A +  L  L +   AY+
Sbjct: 241 TYAMTGWRIGFGAGPQALANAMTVVQSQSTSGASSVGQAAALAAFDGGLDFLRSQVAAYQ 300

Query: 298 RRRDLVIECLADSPGLRPLRPDGGMFVMV-------DIRPTGLSAQAFAD--RLLDRHGV 348
           +RRDL++  L    GL  L P GG FV +         RP G   Q  AD    L   GV
Sbjct: 301 QRRDLLVSALRKVDGLEVLEPQGGFFVFIRCAGLLGRYRPDGQRLQTDADVVAYLLEEGV 360

Query: 349 SVLAGEAFGPSAAGHIRLGLVLGAEPLREACRRIALCAAELLGQ 392
           + +AG A+G S     RL +    E + EA RRIA    +L G+
Sbjct: 361 AGVAGSAYGLSP--WFRLSIATATETVAEAGRRIAQACGQLRGE 402


Lambda     K      H
   0.322    0.136    0.411 

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: 424
Number of extensions: 20
Number of successful extensions: 2
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: 393
Length of database: 403
Length adjustment: 31
Effective length of query: 362
Effective length of database: 372
Effective search space:   134664
Effective search space used:   134664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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