GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Herbaspirillum seropedicae SmR1

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate HSERO_RS19685 HSERO_RS19685 4-aminobutyrate aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__HerbieS:HSERO_RS19685
          Length = 456

 Score =  243 bits (619), Expect = 1e-68
 Identities = 149/444 (33%), Positives = 238/444 (53%), Gaps = 27/444 (6%)

Query: 11  PGPKAKEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGH 70
           PGPK    +E + +  +M  +    +PI +++  G+   D DGN F D ++GVGV +VG 
Sbjct: 23  PGPKTAAALELSARTESMA-RGGGRMPIAMDQAFGVTFKDPDGNTFIDLSAGVGVSSVGR 81

Query: 71  SHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVV--YGNSGAEAN 128
            +PRVVEAI+KQ+E   H    +        LA K+ E+ P  +    +  +   G++A 
Sbjct: 82  CNPRVVEAIRKQSESLMHSMEVNSSKRTE--LAAKISEIMPDGLRGDCITFFTQGGSDAL 139

Query: 129 EAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPY 188
           EAA+K  K  TGR Q +AF+  +HG   A  +LT      + GF P M GV H PYP  Y
Sbjct: 140 EAAVKFAKRVTGRHQIIAFHGGYHGIWNASNALTTGT-AYRKGFGPFMGGVIHAPYPYAY 198

Query: 189 RNTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKA 248
           R  +    ++  +++    +D++    +      ++ A+  EP+QGEGGYV P   F + 
Sbjct: 199 RFPFDTS-HKSAEQIAGEYVDYLLNTPY--TAADDVAAVIVEPVQGEGGYVPPSPEFLQI 255

Query: 249 LKKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRAD 308
           L+K  D  G LL  DEVQ G GRTGK WA+EH GV+PD++ FGK IGG +P+AG++ R+D
Sbjct: 256 LRKACDRSGALLIVDEVQAGAGRTGKMWAVEHSGVKPDMLTFGKGIGGDMPMAGLVMRSD 315

Query: 309 ITFDKP-GRHATTFGGNPVAIAAGIEVVEIVK----ELLPHVQEVGDYLHKYLEEFKEKY 363
           +    P G    TF  N ++ A  +  + I++    +L+     +G    + +  F   +
Sbjct: 316 LAAKIPDGSQPNTFAANSISAAVALTNISILQDPRLDLVNRAHTLGLEAQERIRSFNSPW 375

Query: 364 EVIGDARGLGLAQAVEIVKSKET-----KEKYPELRDRIVKESAKRGLVLLGCG--DNSI 416
             +G+ RG GL   +E+V+++ET     +EK  +L D +V      G++++ CG   N +
Sbjct: 376 --VGEVRGRGLMIGIELVENRETREPLSREKLGKLMDYVV----GHGVLMIPCGRYTNVM 429

Query: 417 RFIPPLIVTKEEIDVAMEIFEEAL 440
           R +P L + +  +   ++IF   L
Sbjct: 430 RVMPSLTIPRSLMFKGLDIFGAGL 453


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: 520
Number of extensions: 38
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: 456
Length adjustment: 33
Effective length of query: 412
Effective length of database: 423
Effective search space:   174276
Effective search space used:   174276
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