GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Paraburkholderia bryophila 376MFSha3.1

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate H281DRAFT_01082 H281DRAFT_01082 putrescine aminotransferase

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



>FitnessBrowser__Burk376:H281DRAFT_01082
          Length = 478

 Score =  877 bits (2266), Expect = 0.0
 Identities = 422/482 (87%), Positives = 456/482 (94%), Gaps = 4/482 (0%)

Query: 1   MSYRTEEVAYVQPAQPAASAQASQAAQQQRSTAEYRALDAAHHIHPFSDMGSLNRSGSRV 60
           MSYRTEE+AY+QPA+PAA A+ +Q    QR+TAEYRALDAAHHIHPFSDMG LNRSGSRV
Sbjct: 1   MSYRTEEIAYMQPAEPAAGARTAQ----QRTTAEYRALDAAHHIHPFSDMGELNRSGSRV 56

Query: 61  IVKAQGVYLWDSEGNKVIDGMAGLWCVNVGYGRKELADAAYKQMQELPYYNTFFKTTHPP 120
           IV+A GVYLWDSEGNK+IDGMAGLWCVNVGYGRKELA+AAY+QM+ELPYYNTFFKTTHPP
Sbjct: 57  IVRAHGVYLWDSEGNKIIDGMAGLWCVNVGYGRKELANAAYRQMEELPYYNTFFKTTHPP 116

Query: 121 VIELSALLAELAPEAFNHFFYCNSGSEGNDTVLRIVHQYWATQGKHSKKFVISRKNGYHG 180
           VIELSALLAELAPE FNHFFYCNSGSE NDTVLRIVH+YW TQGKHSKK VISR+NGYHG
Sbjct: 117 VIELSALLAELAPEPFNHFFYCNSGSEANDTVLRIVHRYWTTQGKHSKKVVISRRNGYHG 176

Query: 181 STIAGGTLGGMGYMHEQMPSKVENIVHIDQPYFFGEAQGNLTPEEFALARAQQLEAKILE 240
           STIAGGTLGGMGYMHEQMPSKVENIVHIDQPYFF EA  + TPEEFALARAQQLE KILE
Sbjct: 177 STIAGGTLGGMGYMHEQMPSKVENIVHIDQPYFFAEANSSQTPEEFALARAQQLEMKILE 236

Query: 241 IGADNVAAFIGEPFQGAGGVIFPASTYWPEIQRICRKYDILLVADEVIGGFGRTGEWFAH 300
           IGA NVAAFIGEPFQGAGGVIFPASTYWPEI+RICRKYD+LLVADEVIGGFGRTGEWFAH
Sbjct: 237 IGAHNVAAFIGEPFQGAGGVIFPASTYWPEIERICRKYDVLLVADEVIGGFGRTGEWFAH 296

Query: 301 QHFGFEPDLITLAKGLTSGYVPMGAVGLHDRVAKAIIENGDFNHGLTYSGHPVAAAVAVA 360
           QHFGF+PDLIT+AKGLTSGYVPMGAVGL+DR+AKAIIENG+FNHGLTYSGHPVAAAVAVA
Sbjct: 297 QHFGFQPDLITMAKGLTSGYVPMGAVGLNDRIAKAIIENGEFNHGLTYSGHPVAAAVAVA 356

Query: 361 NLKLLRDEKIVDRVKNDTGPYFQKQLRETFANHPIIGEISGTGLVAGLQLAQDPKARKRF 420
           NLKLLRDEKIV+RVK DTGPYFQK+LR+TFA HPI+GEI+G GLVAGLQLA++P +RKRF
Sbjct: 357 NLKLLRDEKIVERVKTDTGPYFQKKLRDTFARHPIVGEIAGAGLVAGLQLAEEPASRKRF 416

Query: 421 ANGGDVGTICRDFCFNGNLIMRATGDRMLLSPPLVINKLEIDEIVSKAKKAIDATAQQLG 480
           ANGGDVG +CRDFCFNGNLIMRA+GDRMLLSPPLVI+K EID++VSKAK AIDATA QLG
Sbjct: 417 ANGGDVGGVCRDFCFNGNLIMRASGDRMLLSPPLVISKQEIDDLVSKAKNAIDATATQLG 476

Query: 481 IS 482
           IS
Sbjct: 477 IS 478


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: 834
Number of extensions: 18
Number of successful extensions: 2
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: 478
Length adjustment: 34
Effective length of query: 448
Effective length of database: 444
Effective search space:   198912
Effective search space used:   198912
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