GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Brucella inopinata BO1

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_000182725.1:WP_008507916.1
          Length = 403

 Score =  202 bits (515), Expect = 1e-56
 Identities = 142/413 (34%), Positives = 208/413 (50%), Gaps = 55/413 (13%)

Query: 41  ERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAI 100
           ERGEGI +   DG  + DFA+G+ V ++GHSHP +VE +K QAEK  H S     YE  I
Sbjct: 22  ERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQAEKLWHLSN---IYE--I 76

Query: 101 ILAEKL-IELAPGDIERKVVYGNSGAEANEAAMKLVK---YGTG---RKQFLAFYHAFHG 153
              EKL   L       KV + NSGAEA E A+K  +   Y +G   R + + F  AFHG
Sbjct: 77  PAQEKLGRRLVENTFADKVFFTNSGAEALECAIKTARRYQYVSGHPERFRIITFEGAFHG 136

Query: 154 RTQAVLSLTA-SKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIE 212
           RT A ++    +K+++  GF P + G   +P                          F +
Sbjct: 137 RTLATIAAGGQAKYLE--GFGPKVEGFDQVP--------------------------FGD 168

Query: 213 EYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRT 272
           E   R     E   I  EPIQGEGG    P+ F + +++  DE G+LL  DEVQ G+GRT
Sbjct: 169 EAALRAAITPETAGILLEPIQGEGGLRAFPEEFLRLVRQICDENGLLLLLDEVQTGVGRT 228

Query: 273 GKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFD-KPGRHATTFGGNPVAIAAG 331
           GKF+A E  G+ PD++   K IGGG P+   +  A+       G H TT+GGNP+ +A G
Sbjct: 229 GKFFAHEWAGIRPDIMAIAKGIGGGFPIGACLATAEAAKGMTAGMHGTTYGGNPLGMAVG 288

Query: 332 IEVVEIV--KELLPHVQEVGDYLHKYLEEFKEKY-EVIGDARGLGLAQAVEIVKSKETKE 388
             V+++V     + +VQ     + + L    ++Y  V+ + RG GL   ++ V    +  
Sbjct: 289 NAVLDVVLADGFMENVQATALVMKQGLASLVDRYPNVVSEIRGRGLLMGLKCVVPNTS-- 346

Query: 389 KYPELRDRIVKESAKRGLVLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEALK 441
                   +++      ++ +G GDN +R +PPLI T EE   A++  E A++
Sbjct: 347 --------LIQALRDEHVLSVGAGDNVVRLLPPLITTPEEAREALKHIETAVE 391


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: 497
Number of extensions: 22
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: 403
Length adjustment: 32
Effective length of query: 413
Effective length of database: 371
Effective search space:   153223
Effective search space used:   153223
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 24 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