GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Phaeobacter inhibens BS107

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate GFF767 PGA1_c07810 aminotransferase class-III

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__Phaeo:GFF767
          Length = 457

 Score =  317 bits (811), Expect = 7e-91
 Identities = 164/420 (39%), Positives = 251/420 (59%), Gaps = 9/420 (2%)

Query: 37  RIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREELVQAATRQMRELPFYNLFFQTAH 96
           R++T   G +I D +GN++LDA AGL+CVNVGYGR E+ +A   Q REL +Y+ +     
Sbjct: 33  RVVTGGTGCHIEDRDGNRMLDAFAGLYCVNVGYGRPEIAEAIADQARELAYYHSYVGHGT 92

Query: 97  PPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRMVRHYWATKGQPQKKVVIGRWNGY 156
              + LAK I D AP+ M+ V+F  SGS+AN+T ++++ +Y    G+P+KK +I RW GY
Sbjct: 93  EASITLAKMIMDRAPDHMSKVYFGLSGSDANETNIKLIWYYNNILGRPEKKKIISRWRGY 152

Query: 157 HGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWY-GEGGDMSPDEFGVWAAEQLEKKI 215
           HGS +   SL G++  H + D P+  +VH   PY++  E    S  +F      +LE  I
Sbjct: 153 HGSGLMTGSLTGLELFHNKFDLPLAQVVHTESPYYFRREDLSQSEADFVAHCVAELEALI 212

Query: 216 LEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILAKYDILFIADEVICGFGRTGEWF 275
              G + +AAFI EP+ G GG++ PP  YWP I+ +L ++DIL +ADEV+ GFGR G  F
Sbjct: 213 AREGADTIAAFIGEPVLGTGGIVPPPAGYWPAIQAVLERHDILLVADEVVTGFGRLGTMF 272

Query: 276 GSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVLNQG----GEFYHGFTYSGHPVA 331
           GS +YG  PDL+ IAKGLTS Y P+ G +V D++ +VL +G    G   HG+TYS HP+ 
Sbjct: 273 GSDHYGMRPDLITIAKGLTSAYAPLSGSIVSDKMWQVLERGTDENGPIGHGWTYSAHPIG 332

Query: 332 AAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLVGEARGVGMVAALELVKNKK 391
           AA  + N++++ +  ++E   A  A    +  + L DHP VG+ RG GM+ A+E V ++ 
Sbjct: 333 AAAGVANLKLIDQLGLVENAGAIGAYLNDEMRKALGDHPNVGDLRGEGMLCAVEFVADRD 392

Query: 392 TRERF--TDKGVGMLCREHCFRNGLIMRAV--GDTMIISPPLVIDPSQIDELITLARKCL 447
            R  F  +DK    +  +   ++ +I RA+  GD +  +PP  +   + D ++    + +
Sbjct: 393 DRRFFDASDKIGPQIAAKLLEQDSVIARAMPQGDILGFAPPFCLTRDEADRVVAATHRAV 452


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: 653
Number of extensions: 33
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: 457
Length adjustment: 33
Effective length of query: 423
Effective length of database: 424
Effective search space:   179352
Effective search space used:   179352
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