GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Methanoculleus horonobensis T10

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_067072365.1 MCUHO_RS00805 aspartate aminotransferase family protein

Query= curated2:Q89RB7
         (404 letters)



>NCBI__GCF_001602375.1:WP_067072365.1
          Length = 374

 Score =  236 bits (602), Expect = 8e-67
 Identities = 136/364 (37%), Positives = 195/364 (53%), Gaps = 22/364 (6%)

Query: 29  RGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAFHNDQLAPF 88
           RG G  VWD  G +YLDC++  +  S GHCHP ++ A+  QA  L   S  ++    A  
Sbjct: 25  RGAGSRVWDDRGRQYLDCVAGIAVCSTGHCHPLVVEALCNQAKELIHCSNLYYIPNQAEL 84

Query: 89  YEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADNFHGRTLG 148
            E++  +TG  K    NSGAEA + AIK  R        V   +   +     FHGRT G
Sbjct: 85  AEKLVGITGLSKAFFSNSGAEANDGAIKLAR--------VRTGRKNFVAFTHGFHGRTCG 136

Query: 149 IVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAGVIIPPAG 208
            +  +  P  R  F P +     + +GD  AL +A+  +T    VEPIQGEAGV+IPP  
Sbjct: 137 SLAVTHKPAIREPFEPLSTPCTFVDYGDLDALAKAVNKDTAGVFVEPIQGEAGVLIPPDE 196

Query: 209 YFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALAGGFYPVSAV 268
           +   VR++C     ++++DE+QTG+GRTGK  A QH GI  D+    K LA GF P+ A+
Sbjct: 197 FLRGVRDICDDTGALMIVDEVQTGMGRTGKWFAFQHAGILPDIVTTAKGLASGF-PIGAL 255

Query: 269 LSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLLEGLKDIR 328
           ++   +    + G+HGSTF G PLACA A A + V+  E ++ +  R+G R  +GL   R
Sbjct: 256 VAREGL--EFKKGEHGSTFAGGPLACATALATIGVI--EEILPDVTRKGERFKKGL--AR 309

Query: 329 ANTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTIRIAPPLVITSDEV 388
            N     RGRGL++ + +       ++ C A    G+L        +R+ PPLVIT +E+
Sbjct: 310 HNP----RGRGLIIGMSIGDRCAEVQQTCAA---NGVLVNCAADGNLRLIPPLVITDNEI 362

Query: 389 DWAL 392
           D AL
Sbjct: 363 DCAL 366


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: 435
Number of extensions: 23
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: 374
Length adjustment: 30
Effective length of query: 374
Effective length of database: 344
Effective search space:   128656
Effective search space used:   128656
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