GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Marinobacter adhaerens HP15

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__Marino:GFF3766
          Length = 425

 Score =  264 bits (674), Expect = 5e-75
 Identities = 157/433 (36%), Positives = 235/433 (54%), Gaps = 22/433 (5%)

Query: 16  KEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRV 75
           KE+     +Y+A     P       +      ++D DG    DFA G+GV+N+GH HP+V
Sbjct: 4   KELQALKERYVAAGAASPNEQ--FADHATNAELWDADGKRMIDFAGGIGVLNIGHRHPKV 61

Query: 76  VEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLV 135
           VEA+K Q +K  H   T   YE  + LAEKL  + P     KV+  NSGAEA E AMK+ 
Sbjct: 62  VEAVKAQLDKLMHTCQTVMPYEGYVKLAEKLSGVVPVRGHAKVMLANSGAEALENAMKIA 121

Query: 136 KYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPG-VTHIPYPNPYRNTWGI 194
           +  TG+   + F   +HGRT   +++       Q  F P MPG V   PYP PY      
Sbjct: 122 RAATGKTNVICFDGGYHGRTFYTMAMNGKAAPYQTDFGP-MPGTVYRAPYPVPYH----- 175

Query: 195 DGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFAD 254
            G  E + L       ++  +    P H   AI  EP+ GEGG+   P  F K ++K  D
Sbjct: 176 -GVSEDEALRG-----LKMAMKADSPAHNTAAIVIEPVLGEGGFYAAPTSFLKEIRKICD 229

Query: 255 EYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKP 314
           E  IL+  DEVQ G GRTGK +AIEH GVEPDL+   K++  G+P++ ++   D   D  
Sbjct: 230 ENDILMIADEVQSGFGRTGKMFAIEHSGVEPDLMTMAKSMADGMPISAIV-GTDKYMDAS 288

Query: 315 GRHAT--TFGGNPVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDAR 370
           G ++   T+ G+P A AA + V ++ KE  +L   Q +G+ L +   +++E++  + + R
Sbjct: 289 GPNSLGGTYTGSPTACAAALAVFDVFKEEDILGKSQALGEKLKQRFSQWQEQFAHVDNVR 348

Query: 371 GLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEE 428
            LG   A E+V+SKE++   PEL   + K++ ++GL+LL CG   N++RF+ P+ +  E 
Sbjct: 349 NLGPMAAFELVESKESRTPKPELAAAVTKKAKEKGLILLSCGMYGNTLRFLMPVTIEDEV 408

Query: 429 IDVAMEIFEEALK 441
           ++  + I EE+LK
Sbjct: 409 LEEGLAIVEESLK 421


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: 528
Number of extensions: 24
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: 445
Length of database: 425
Length adjustment: 32
Effective length of query: 413
Effective length of database: 393
Effective search space:   162309
Effective search space used:   162309
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