Alignments for a candidate for gabT in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Pseudomonas putida KT2440

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate PP_2588 PP_2588 Aminotransferase, class III

Query= reanno::BFirm:BPHYT_RS23155
         (482 letters)



>FitnessBrowser__Putida:PP_2588
          Length = 460

 Score =  553 bits (1425), Expect = e-162
 Identities = 267/453 (58%), Positives = 336/453 (74%), Gaps = 3/453 (0%)

Query: 29  QRSTAEYRALDAAHHIHPFSDMGSLNRSGSRVIVKAQGVYLWDSEGNKVIDGMAGLWCVN 88
           QR T +Y+A DAAHHIH F D  +LN  G RVIV  + ++LWDSEG + +DGM+GLWC  
Sbjct: 8   QRQTRDYQAADAAHHIHAFLDQKALNAEGPRVIVGGERLHLWDSEGKRYLDGMSGLWCTQ 67

Query: 89  VGYGRKELADAAYKQMQELPYYNTFFKTTHPPVIELSALLAELAPEAFNHFFYCNSGSEG 148
           +GYGR++L  AA  QM +L YYN FF TTHP VIELS LL  L P  ++H  Y NSGSE 
Sbjct: 68  LGYGRRDLTAAAATQMDQLAYYNMFFHTTHPAVIELSELLFSLLPGHYSHAIYTNSGSEA 127

Query: 149 NDTVLRIVHQYWATQGKHSKKFVISRKNGYHGSTIAGGTLGGMGYMHEQMPSKVENIVHI 208
           N+ ++R V +YW   G+  KK +I R NGYHGST+A   LGGM +MH+ M   + ++ HI
Sbjct: 128 NEVLIRTVRRYWQVVGQPGKKIMIGRWNGYHGSTLAATALGGMKFMHD-MGGLIPDVAHI 186

Query: 209 DQPYFFGEAQGNLTPEEFALARAQQLEAKILEIGADNVAAFIGEPFQGAGGVIFPASTYW 268
           D+PY++ E  G LTP EF    A QLE KILE+GA+NVA FI EPFQGAGG+IFP  +YW
Sbjct: 187 DEPYWYAEG-GELTPAEFGRRCALQLEEKILELGAENVAGFIAEPFQGAGGMIFPPESYW 245

Query: 269 PEIQRICRKYDILLVADEVIGGFGRTGEWFAHQHFGFEPDLITLAKGLTSGYVPMGAVGL 328
           PEIQRICR+YD+LL ADEVIGGFGRTGEWFAH++FGFEPD +++AKGLTSGYVPMG + L
Sbjct: 246 PEIQRICRQYDVLLCADEVIGGFGRTGEWFAHEYFGFEPDTLSIAKGLTSGYVPMGGLVL 305

Query: 329 HDRVAKAIIENGD-FNHGLTYSGHPVAAAVAVANLKLLRDEKIVDRVKNDTGPYFQKQLR 387
             R+A+A++E G  F HGLTYSGHPVAAAVA+ANLK LRDE IV +VK+DTGPY Q+ LR
Sbjct: 306 SKRIAEALVERGGVFAHGLTYSGHPVAAAVAIANLKALRDEGIVRQVKDDTGPYLQRILR 365

Query: 388 ETFANHPIIGEISGTGLVAGLQLAQDPKARKRFANGGDVGTICRDFCFNGNLIMRATGDR 447
           E FA+HP+IG++ G GLVA LQ A+    RKRFAN  D+   CR F F   +I+R+T  R
Sbjct: 366 EVFADHPLIGQVQGAGLVAALQFAEHKPTRKRFANENDLAWQCRTFGFEEGVIIRSTLGR 425

Query: 448 MLLSPPLVINKLEIDEIVSKAKKAIDATAQQLG 480
           M+++P L+ N  E+DE+V K + A+D TA+ +G
Sbjct: 426 MIMAPALIANHSELDELVEKTRIAVDRTARLVG 458


Lambda     K      H
   0.319    0.136    0.408 

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: 641
Number of extensions: 30
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: 482
Length of database: 460
Length adjustment: 33
Effective length of query: 449
Effective length of database: 427
Effective search space:   191723
Effective search space used:   191723
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources