GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patA in Burkholderia phytofirmans PsJN

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate BPHYT_RS23155 BPHYT_RS23155 aminotransferase

Query= BRENDA::Q9I6J2
         (456 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS23155 BPHYT_RS23155
           aminotransferase
          Length = 482

 Score =  558 bits (1437), Expect = e-163
 Identities = 259/445 (58%), Positives = 342/445 (76%), Gaps = 3/445 (0%)

Query: 10  TREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGY 69
           T E++AL   HH+ PF+D   LN  G+R+I KA+GVY+WDSEGNK++D MAGLWCVNVGY
Sbjct: 32  TAEYRALDAAHHIHPFSDMGSLNRSGSRVIVKAQGVYLWDSEGNKVIDGMAGLWCVNVGY 91

Query: 70  GREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDT 129
           GR+EL  AA +QM+ELP+YN FF+T HPPV+EL+  +A++APE  NH F+  SGSE NDT
Sbjct: 92  GRKELADAAYKQMQELPYYNTFFKTTHPPVIELSALLAELAPEAFNHFFYCNSGSEGNDT 151

Query: 130 VLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQP 189
           VLR+V  YWAT+G+  KK VI R NGYHGST+AG +LGGM  +HEQ    +  IVHI QP
Sbjct: 152 VLRIVHQYWATQGKHSKKFVISRKNGYHGSTIAGGTLGGMGYMHEQMPSKVENIVHIDQP 211

Query: 190 YWYGEG-GDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKI 248
           Y++GE  G+++P+EF +  A+QLE KILE+G +NVAAFI EP QGAGGVI P  TYWP+I
Sbjct: 212 YFFGEAQGNLTPEEFALARAQQLEAKILEIGADNVAAFIGEPFQGAGGVIFPASTYWPEI 271

Query: 249 REILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDE 308
           + I  KYDIL +ADEVI GFGRTGEWF  Q++G  PDL+ +AKGLTSGY+PMG V + D 
Sbjct: 272 QRICRKYDILLVADEVIGGFGRTGEWFAHQHFGFEPDLITLAKGLTSGYVPMGAVGLHDR 331

Query: 309 IVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQE-LA 367
           + + + + G+F HG TYSGHPVAAAVA+ N+++LR+EKI+++VK +T PY QK+ +E  A
Sbjct: 332 VAKAIIENGDFNHGLTYSGHPVAAAVAVANLKLLRDEKIVDRVKNDTGPYFQKQLRETFA 391

Query: 368 DHPLVGEARGVGMVAALELVKNKKTRERFTDKG-VGMLCREHCFRNGLIMRAVGDTMIIS 426
           +HP++GE  G G+VA L+L ++ K R+RF + G VG +CR+ CF   LIMRA GD M++S
Sbjct: 392 NHPIIGEISGTGLVAGLQLAQDPKARKRFANGGDVGTICRDFCFNGNLIMRATGDRMLLS 451

Query: 427 PPLVIDPSQIDELITLARKCLDQTA 451
           PPLVI+  +IDE+++ A+K +D TA
Sbjct: 452 PPLVINKLEIDEIVSKAKKAIDATA 476


Lambda     K      H
   0.320    0.138    0.425 

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: 716
Number of extensions: 35
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: 456
Length of database: 482
Length adjustment: 33
Effective length of query: 423
Effective length of database: 449
Effective search space:   189927
Effective search space used:   189927
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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