GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Sinorhizobium meliloti 1021

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate SM_b21186 SM_b21186 4-aminobutyrate aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>lcl|FitnessBrowser__Smeli:SM_b21186 SM_b21186 4-aminobutyrate
           aminotransferase
          Length = 422

 Score =  261 bits (666), Expect = 4e-74
 Identities = 155/423 (36%), Positives = 227/423 (53%), Gaps = 23/423 (5%)

Query: 26  LAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEK 85
           + MTTQ      +  +R E   ++D +GN + DFA+G+ V+N GH HP+V+ A+K Q ++
Sbjct: 16  VGMTTQ------VYADRAENAEIWDKEGNRYIDFAAGIAVVNTGHRHPKVIAAVKAQLDR 69

Query: 86  FTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFL 145
           FTH       YEN + LAE+L  + PGD  +K ++  +GAEA E A+K+ +  TGR+  +
Sbjct: 70  FTHTCHQVVPYENYVHLAERLNAIVPGDFAKKTIFVTTGAEAVENAVKIARAATGRQAVV 129

Query: 146 AFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTN 205
           AF   FHGRT   ++LT      + GF      V H P+P            E       
Sbjct: 130 AFGGGFHGRTFMGMALTGKVVPYKVGFGAMPADVFHAPFP-----------IELHGVTVE 178

Query: 206 RVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEV 265
           + L  +++     V P  + AI  EP+QGEGG+   P  F KAL++  D++GILL  DEV
Sbjct: 179 QSLSALKKLFAADVDPARVAAIIIEPVQGEGGFYPVPTAFMKALREVCDQHGILLIADEV 238

Query: 266 QMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGN 324
           Q G  RTGK +A+EH GV PDL    K++ GG PLA V  RA+I     PG    T+GGN
Sbjct: 239 QTGFARTGKLFAMEHHGVAPDLTTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLGGTYGGN 298

Query: 325 PVAIAAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVK 382
           P+ IAA   V++++ E  L     ++G+ L + L   +EK   I D RG G   AVE   
Sbjct: 299 PLGIAAAHAVLDVIAEENLCERANQLGNRLKQRLAAIREKAPEIVDIRGPGFMNAVEF-N 357

Query: 383 SKETKEKYPELRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEAL 440
              T     E  +++   + ++GL+LL CG   N IRF+ P+ +  E    A++  E ++
Sbjct: 358 DVRTNLPSAEFANKVRLLALEKGLILLTCGVHGNVIRFLAPITIQDEVFAEALDTIEASI 417

Query: 441 KAA 443
             A
Sbjct: 418 LEA 420


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: 494
Number of extensions: 28
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: 422
Length adjustment: 32
Effective length of query: 413
Effective length of database: 390
Effective search space:   161070
Effective search space used:   161070
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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