GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Methanospirillum lacunae Ki8-1

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_109969613.1 DK846_RS14130 acetylornithine transaminase

Query= curated2:Q89RB7
         (404 letters)



>NCBI__GCF_003173355.1:WP_109969613.1
          Length = 384

 Score =  244 bits (623), Expect = 3e-69
 Identities = 140/370 (37%), Positives = 203/370 (54%), Gaps = 25/370 (6%)

Query: 25  VVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQAHRLTLTSRAF---H 81
           +++++G G  V D DG +YLD ++  +  S GHCHPK++ A+ EQA  L   S  F   H
Sbjct: 23  IMITKGSGCTVTDADGKQYLDLVAGIAVCSTGHCHPKVVKAIAEQAAELIHCSNLFYVPH 82

Query: 82  NDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVKGVPDDQAEIIVCADN 141
              LA    EI+ L G+ K    NSGAEA+E A+K  R        +   + E I C   
Sbjct: 83  QGALAKKLVEISGLPGNAKAFFSNSGAEAMEGALKLAR--------IRTGRKEFIACEGG 134

Query: 142 FHGRTLGIVGFSTDPETRGHFGPFAPGFRIIPFGDAAALEQAITPNTVAFLVEPIQGEAG 201
           FHGRT+G +  +  P  R  F P  P    +P+GD  AL+ AIT  T A ++EPIQGE G
Sbjct: 135 FHGRTMGSLACTHKPAIREPFMPLQPFTSFVPYGDVQALKGAITEETAAVILEPIQGEGG 194

Query: 202 VIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRTGKLLAEQHEGIEADVTLLGKALAGG 261
           VIIPP GY  +VRE+C A  V+L++DE+Q+G+GRTG   A Q EGI  D+  + KA+A G
Sbjct: 195 VIIPPPGYLKQVREICDAKGVLLIVDEVQSGMGRTGHWFAFQEEGIHPDIITMAKAMASG 254

Query: 262 FYPVSAVLSNNEVLGTLRPGQHGSTFGGNPLACAVARAAMRVLVEEGMIENAARQGARLL 321
           F P+ A+++   +       +HGSTF G P+ACA A A++ V+ +  ++   A +G R  
Sbjct: 255 F-PMGAIVAREGL--EFGKSEHGSTFAGGPIACAAALASIDVIGK--VLPEVAAKGERFR 309

Query: 322 EGLKDIRANTVREVRGRGLMLAVELHPEAGRARRYCEALQGKGILAKDTHGHTIRIAPPL 381
             L  +        R +GLM+ + +       ++ C      G+L        +R+ PPL
Sbjct: 310 AALAHLNP------RVKGLMIGITIGDHCADVQKECAV---HGLLVNCAAHGNLRLVPPL 360

Query: 382 VITSDEVDWA 391
            IT+ E+D A
Sbjct: 361 TITNAEIDKA 370


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: 454
Number of extensions: 19
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: 404
Length of database: 384
Length adjustment: 31
Effective length of query: 373
Effective length of database: 353
Effective search space:   131669
Effective search space used:   131669
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.

Links

Downloads

Related tools

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