GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Nocardioides daejeonensis MJ31

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_110205831.1 DNK54_RS04735 acetylornithine transaminase

Query= curated2:Q89RB7
         (404 letters)



>NCBI__GCF_003194585.1:WP_110205831.1
          Length = 396

 Score =  261 bits (666), Expect = 3e-74
 Identities = 152/383 (39%), Positives = 209/383 (54%), Gaps = 21/383 (5%)

Query: 25  VVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAFHNDQ 84
           +VL++GEG  VWD DGN YLD L   +    GH HP ++ A+ +Q   L   S  F +  
Sbjct: 24  LVLAKGEGATVWDADGNEYLDLLGGIAVNLLGHAHPALIEAVTQQLGTLGHVSNFFTSGP 83

Query: 85  LAPFYEEIAALTGSH-KVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADNFH 143
                E + AL G   +V   NSG EA E+A K  R+ G         +  ++     FH
Sbjct: 84  QVELAERLLALLGQDGRVFLSNSGTEANEAAFKITRRTG---------RTHVVATEGGFH 134

Query: 144 GRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAGVI 203
           GRT+G +  ++    R  F P       +P+GDAAALE A+T  T A ++EPIQGEAGV 
Sbjct: 135 GRTMGALALTSKAAYRDPFAPLPGDVTFVPYGDAAALEAAVTDQTAAVVLEPIQGEAGVN 194

Query: 204 IPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEG-----IEADVTLLGKAL 258
           +PP+ Y  +VRE+ + +  ++ LDEIQTG+GRTG+  A QH G     +  D+  L K L
Sbjct: 195 VPPSDYLARVREITSRHGALMWLDEIQTGVGRTGRWFAHQHPGLAPEPVTPDLITLAKGL 254

Query: 259 AGGFYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGA 318
            GG  P+ A ++       L+PGQHG+TFGGNP+A A A A +RV  EE ++  A   G 
Sbjct: 255 GGGL-PIGATIALGAAGDLLQPGQHGTTFGGNPVATAAALAVLRVAEEESLLARAEALGE 313

Query: 319 RLLEGLKDIRANTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTIRIA 378
           RL  GL D R   V EVRG GL++ ++L  E  R+     A  G G +  +   H IR+A
Sbjct: 314 RLRAGLADPR---VSEVRGLGLLIGLDLAQE--RSAEVAAAALGAGFIINNPTPHRIRLA 368

Query: 379 PPLVITSDEVDWALEQFATTLTQ 401
           PPLV+T  + D  L  +   L Q
Sbjct: 369 PPLVLTDAQADRFLAAWPGILDQ 391


Lambda     K      H
   0.319    0.136    0.405 

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: 465
Number of extensions: 24
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: 404
Length of database: 396
Length adjustment: 31
Effective length of query: 373
Effective length of database: 365
Effective search space:   136145
Effective search space used:   136145
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 (21.8 bits)
S2: 50 (23.9 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