GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Rhodanobacter denitrificans FW104-10B01

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_027490801.1 LRK54_RS04500 acetyl ornithine aminotransferase family protein

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_021560695.1:WP_027490801.1
          Length = 444

 Score =  351 bits (901), Expect = e-101
 Identities = 188/437 (43%), Positives = 263/437 (60%), Gaps = 11/437 (2%)

Query: 10  LPGPKAKEVIERNFKYLAMTTQDPENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVG 69
           LPGPKA+ +I R+ + ++ +   P + P V+  G G  V+DVDGN F DF +G+ V   G
Sbjct: 14  LPGPKAQAMIARDAEVISPSY--PRDYPFVMSHGRGTEVWDVDGNRFLDFMAGIAVCATG 71

Query: 70  HSHPRVVEAIKKQAEKFTHYSLTDFFYENAIILAEKLIELAPGDIERKVVYGNSGAEANE 129
           H+HP+VV+A++  A KF H S +D+++E    L E+L  +AP           SG EA E
Sbjct: 72  HAHPQVVKAVQDAAAKFLHIS-SDYWHEEMTGLGERLAAVAPLGAPAMSFICQSGTEAVE 130

Query: 130 AAMKLVKYGTGRKQFLAFYHAFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYR 189
            A+KL +Y TGR +F+ F   FHGRT   LS T+SK+ QQ GF PT+ GVTH+PYPNPYR
Sbjct: 131 GALKLARYVTGRPRFIGFLGGFHGRTFGSLSFTSSKYTQQKGFSPTLAGVTHVPYPNPYR 190

Query: 190 NTWGIDGYEEPDELTNRVLDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKAL 249
             +        D+    VLD+I     R VPP E+ AI  EP+QGEGGY+ PP GF   L
Sbjct: 191 PLFA------GDDQGAAVLDYIRMLFQRSVPPSEVAAILIEPMQGEGGYLTPPDGFLAGL 244

Query: 250 KKFADEYGILLADDEVQMGIGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI 309
           +   DE+GILL  DEVQ GIGRTG+ +A EH+GV+PD+I   K +G GLP+  VI +  I
Sbjct: 245 RALCDEHGILLIFDEVQSGIGRTGRMFACEHWGVQPDIITSAKGLGSGLPIGAVIAKKSI 304

Query: 310 TFD-KPGRHATTFGGNPVAIAAGIEVVEIVK-ELLPHVQEVGDYLHKYLEEFKEKYEVIG 367
               K G H  T+GGNPV  AA    +++V+  L+ +   VGD+    L E +  Y  IG
Sbjct: 305 MSQWKRGAHGNTYGGNPVTCAAANATLDLVRGGLMDNAARVGDHFMARLRELQRDYPCIG 364

Query: 368 DARGLGLAQAVEIVKSKETKEKYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKE 427
           + RG GL   +E+++    K     L + +V+ +   GL+LL CG +++RF+PPL V+  
Sbjct: 365 EVRGKGLWIGMELIEDDGKKTPATALCEAVVQRAFHNGLLLLSCGTSTVRFMPPLNVSVG 424

Query: 428 EIDVAMEIFEEALKAAL 444
           E+D A+ +   +L  AL
Sbjct: 425 EVDEAIALLRSSLDQAL 441


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: 530
Number of extensions: 35
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: 444
Length adjustment: 32
Effective length of query: 413
Effective length of database: 412
Effective search space:   170156
Effective search space used:   170156
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 Apr 09 2024. 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