GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Halioglobus japonicus S1-36

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate WP_102106348.1 C0029_RS13280 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::Q5JEW1
         (445 letters)



>NCBI__GCF_002869505.1:WP_102106348.1
          Length = 454

 Score =  177 bits (450), Expect = 5e-49
 Identities = 133/437 (30%), Positives = 221/437 (50%), Gaps = 51/437 (11%)

Query: 39  VIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY-- 96
           V+ R E I +Y  +G+   D  SG+   N+G+S   +V+A+ +Q  +  +Y+  +FF   
Sbjct: 35  VMSRAEHIYIYTAEGHKMLDGMSGLWCCNLGYSQRSIVDAVTEQLGQLPYYN--NFFQCS 92

Query: 97  -ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKY------GTGRKQFLAFYH 149
            + AI LA+ L+++ P      V + NSG+EAN+  ++LV           +K  ++  +
Sbjct: 93  NQPAIELAKALVDITPERFNH-VFFTNSGSEANDTNLRLVSRYYQCQGRPEKKLIISRKN 151

Query: 150 AFHGRTQAVLSL--TASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRV 207
           A+HG T A   L        Q +G    +  V HI  P+ +     +   E+P+E   RV
Sbjct: 152 AYHGSTIAAACLGGMGPMHEQTNG----IDYVHHIEQPHWFE----VGPDEDPNEFGLRV 203

Query: 208 LDFIEEYVFRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQM 267
              +EE +   +    + A   EP+QG GG ++PP  ++  +++  +E  ILL  DEV  
Sbjct: 204 ARQLEEKI-DELGEENVAAFIAEPVQGAGGVIIPPDSYWPEVQRICNERDILLIADEVIC 262

Query: 268 GIGRTGKFWAIEHFGVEPDLIQFGKAIGGGL-PLAGVI---HRADITFDKPGR--HATTF 321
           G GRTG++W  E +G+EPDL+ F KA+  G  PL GV+     AD+     G   H  T+
Sbjct: 263 GFGRTGQWWGSETYGIEPDLMTFAKAVTNGFQPLGGVMVADKVADVLLAHEGEFAHGLTY 322

Query: 322 GGNPVAIAAGIEVVEIVKE---LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAV 378
            G+P A AAG+  + I+KE   +      +  +  + L+E  + ++++G  RG G+  AV
Sbjct: 323 SGHPAAAAAGLATLNILKEGNVIADAAANIAPHFQRRLQELAD-HKIVGQVRGRGMFAAV 381

Query: 379 EIVKSKETKEKYPELRDRIVKESA----------KRGLVLLGCGDNSIRFIPPLIVTKEE 428
           E+VK K ++E        +  ESA          + GL++   G N++   PPLI +  E
Sbjct: 382 ELVKDKSSREP-------LAAESAGALFCRNTANELGLMVRQTG-NAMIMAPPLICSTSE 433

Query: 429 IDVAMEIFEEALKAALK 445
           ID  +++  +AL    K
Sbjct: 434 IDSLIDMLGQALDVTAK 450


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: 505
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: 454
Length adjustment: 33
Effective length of query: 412
Effective length of database: 421
Effective search space:   173452
Effective search space used:   173452
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