GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS23155
          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.

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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