Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N2E3

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate AO353_15040 AO353_15040 aminotransferase

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



>FitnessBrowser__pseudo3_N2E3:AO353_15040
          Length = 456

 Score =  574 bits (1479), Expect = e-168
 Identities = 272/452 (60%), Positives = 341/452 (75%), Gaps = 3/452 (0%)

Query: 30  RSTAEYRALDAAHHIHPFSDMGSLNRSGSRVIVKAQGVYLWDSEGNKVIDGMAGLWCVNV 89
           R T +Y+A DAAHHIH F D  +LN  G RV+V+   ++LWD++G + +DGM+GLWC N+
Sbjct: 5   RETRDYQAADAAHHIHAFVDQKALNDEGPRVMVRGDRLHLWDNDGRRYLDGMSGLWCTNL 64

Query: 90  GYGRKELADAAYKQMQELPYYNTFFKTTHPPVIELSALLAELAPEAFNHFFYCNSGSEGN 149
           GYGRK+LA AA +Q+++LPYYN FF TTHP VIELS LL  L P  ++H  Y NSGSE N
Sbjct: 65  GYGRKDLAAAASRQLEQLPYYNMFFHTTHPQVIELSELLFSLLPGHYSHAIYTNSGSEAN 124

Query: 150 DTVLRIVHQYWATQGKHSKKFVISRKNGYHGSTIAGGTLGGMGYMHEQMPSKVENIVHID 209
           + ++R V +YW   GK  KK +I R NGYHGST+A   LGGM +MHE M   + +I HID
Sbjct: 125 EVLIRTVRRYWTILGKPEKKVMIGRWNGYHGSTLAATALGGMKFMHE-MGGMIPDIAHID 183

Query: 210 QPYFFGEAQGNLTPEEFALARAQQLEAKILEIGADNVAAFIGEPFQGAGGVIFPASTYWP 269
           +PYFF   +GNLTP EF L  AQQLE KILE+GAD VA FI EPFQGAGG+IFP  +YWP
Sbjct: 184 EPYFFAH-EGNLTPAEFGLRAAQQLEEKILELGADKVAGFIAEPFQGAGGMIFPPESYWP 242

Query: 270 EIQRICRKYDILLVADEVIGGFGRTGEWFAHQHFGFEPDLITLAKGLTSGYVPMGAVGLH 329
           EIQRICRKYD+LL ADEVIGGFGRTGEWFAH+HFGFEPD +++AKGLTSGY+PMG + L 
Sbjct: 243 EIQRICRKYDVLLCADEVIGGFGRTGEWFAHEHFGFEPDTLSIAKGLTSGYIPMGGLVLS 302

Query: 330 DRVAKAIIENGD-FNHGLTYSGHPVAAAVAVANLKLLRDEKIVDRVKNDTGPYFQKQLRE 388
            ++A+ ++E G  F HGLTYSGHPVAAAVA+ANLK LRDE +V RVK+D GPY QK LRE
Sbjct: 303 KKMAQVLVEQGGVFAHGLTYSGHPVAAAVAIANLKALRDEGVVTRVKDDIGPYLQKCLRE 362

Query: 389 TFANHPIIGEISGTGLVAGLQLAQDPKARKRFANGGDVGTICRDFCFNGNLIMRATGDRM 448
            F NHP++G+I G G+VA LQLA+D  +RKRFAN  D+   CR   F   +I+R+T  RM
Sbjct: 363 VFGNHPLVGDIQGVGMVAALQLAEDKTSRKRFANENDIAWRCRTIGFEEGVIIRSTLGRM 422

Query: 449 LLSPPLVINKLEIDEIVSKAKKAIDATAQQLG 480
           +++P L+  + E+DE+V K  +A+D TAQ+ G
Sbjct: 423 IMAPALIATREEVDELVGKTLRAVDRTAQEYG 454


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: 651
Number of extensions: 29
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: 456
Length adjustment: 33
Effective length of query: 449
Effective length of database: 423
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 Apr 09 2024. 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 2024 update 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