GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Dinoroseobacter shibae DFL-12

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 3608649 Dshi_2042 aminotransferase class-III (RefSeq)

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__Dino:3608649
          Length = 460

 Score =  199 bits (505), Expect = 2e-55
 Identities = 137/430 (31%), Positives = 217/430 (50%), Gaps = 37/430 (8%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASG-VGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFF 95
           P +I  G+G+RV+D  G    D  SG +  +NVG+   R+  A++ Q  +   +S +   
Sbjct: 36  PRIIVEGKGMRVWDALGKEHLDAVSGGLWTVNVGYGRERIANAVRDQLMQMCFFSNSLGT 95

Query: 96  YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVK------YGTGRKQFLAFYH 149
              AI  +E LI+  PG    +V Y +SG+EANE A K+V+      +G  + + L    
Sbjct: 96  IPGAIF-SEMLIDKMPG--MSRVYYASSGSEANEKAFKMVRQIAHKVHGGRKTKILYRER 152

Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209
            +HG T A +S    +W ++  + P  P    +P+   YR  W  + Y E      R  D
Sbjct: 153 DYHGSTLATMS-AGGQWERKAQYGPFAPDFVEVPHCLEYRAQWEGENYGE------RAAD 205

Query: 210 FIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGI 269
            IEE + R   P  +GA+  EP+   GG + PP+G++  +++   +Y +LL  DEV  G+
Sbjct: 206 AIEEVILRE-GPDTVGALCLEPVTAGGGVITPPEGYWPRVQEICRKYDVLLHIDEVVCGL 264

Query: 270 GRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD----KPG------RHAT 319
           GRTGK++  +H+G+EPD +   K +  G      +   +  F+    +PG      R  +
Sbjct: 265 GRTGKWFGYQHYGIEPDFVTMAKGVASGYAAISCMVTTERVFEMFKSEPGAPLDYFRDIS 324

Query: 320 TFGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQA 377
           TFGG     AA IE ++I++E  LL +   + D L   L    EK+ VIGD RG GL   
Sbjct: 325 TFGGCTAGPAAAIENMKIIEEEDLLGNTDRMHDQLMGNLAGLMEKHRVIGDIRGKGLFCG 384

Query: 378 VEIVKSKETKEKYPE-LRDRIVKESAKRGLVL------LGCGDNSIRFIPPLIVTKEEID 430
            E+V  + TKE  PE L   +V +   +G+++      L   +N++ F P LI T ++ID
Sbjct: 385 AELVADRTTKEPAPEALVQAVVADCMAQGVIIGATNRSLPGYNNTLCFSPALIATADDID 444

Query: 431 VAMEIFEEAL 440
              +  + AL
Sbjct: 445 QITDAVDGAL 454


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: 526
Number of extensions: 26
Number of successful extensions: 6
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: 460
Length adjustment: 33
Effective length of query: 412
Effective length of database: 427
Effective search space:   175924
Effective search space used:   175924
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