GapMind for catabolism of small carbon sources

 

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

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate H281DRAFT_03179 H281DRAFT_03179 4-aminobutyrate aminotransferase apoenzyme

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__Burk376:H281DRAFT_03179
          Length = 429

 Score =  275 bits (702), Expect = 3e-78
 Identities = 161/406 (39%), Positives = 229/406 (56%), Gaps = 17/406 (4%)

Query: 41  ERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAI 100
           ER +   ++DV+G  F DFA+G+ V N GH HP++V AI+ Q ++FTH +     Y + +
Sbjct: 29  ERAQNAELWDVEGRRFIDFAAGIAVCNTGHRHPKIVAAIRDQLDRFTHTAYQIVPYASYV 88

Query: 101 ILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLS 160
            LAEKL E APGD  +K  +  +GAEA E A+K+ +  TGR   +AF   FHGRT   ++
Sbjct: 89  ELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARAATGRPGVIAFTGGFHGRTLMGMA 148

Query: 161 LTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVP 220
           LT      + GF P    V H P+PNP      + G    D L  + ++F+ +     + 
Sbjct: 149 LTGKVAPYKAGFGPFPSDVFHAPFPNP------LHGVSTADSL--KAIEFLFK---ADID 197

Query: 221 PHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEH 280
           P  + AI FEP+QGEGG+   P  F +AL+K  +E+GILL  DEVQ G  RTGK +A+ H
Sbjct: 198 PKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHH 257

Query: 281 FGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIVK 339
           + V PDL+   K++ GG+PL+GVI RAD+     PG    T+ GNP+A+AA + V++I+ 
Sbjct: 258 YDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAALAVLDIID 317

Query: 340 E--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRI 397
           E  L      +GD +   L   + +   I D RG G   AVE  K   T E   E   R+
Sbjct: 318 EEKLCERATILGDRVKAKLIALQNEAPQIADVRGPGGMVAVEFCKPGST-EPDAEFTKRV 376

Query: 398 VKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALK 441
              + KRGL+LL CG   N +RF+ PL +     D A+ I E+ +K
Sbjct: 377 QTRALKRGLLLLVCGVYSNVVRFLFPLTIEDTVFDEALAILEDVIK 422


Lambda     K      H
   0.320    0.141    0.418 

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: 511
Number of extensions: 26
Number of successful extensions: 5
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: 445
Length of database: 429
Length adjustment: 32
Effective length of query: 413
Effective length of database: 397
Effective search space:   163961
Effective search space used:   163961
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 (21.7 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