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 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