GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Sphingomonas koreensis DSMZ 15582

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate Ga0059261_0076 Ga0059261_0076 aspartate carbamoyltransferase (EC 2.1.3.2)

Query= curated2:A0RUE9
         (301 letters)



>FitnessBrowser__Korea:Ga0059261_0076
          Length = 330

 Score =  107 bits (267), Expect = 4e-28
 Identities = 91/295 (30%), Positives = 135/295 (45%), Gaps = 29/295 (9%)

Query: 9   LTGAE-LDRKEILGIIESAIRLKKGGRSKA---HPLDGRTLAMVFQKPSTRTRVSFAAGM 64
           LTG   L   EIL +++ A +  +  RS+A   H LDG T    F + STRT +SF    
Sbjct: 24  LTGISGLQPHEILFLLDEAEQWIEANRSRAKSDHRLDGLTQINAFFENSTRTLLSFEIAG 83

Query: 65  FQLGGEAIYLPPGDMQLSRGETIPDTARALSGY-VDVIVARVFGHETIEEIAASASVPVI 123
            +LG + + +      + +GET+ DTA  L+    DVIV R      ++ IA     PV+
Sbjct: 84  KRLGADVVNMHAAQSSVKKGETLIDTAMTLNAMRADVIVIRHMSSGAVQLIADKVDCPVL 143

Query: 124 N-GLSDTFHPCQILADLMTIKERKGRLKGLRAAWIGD--GNNVCNSLLYGCAAVGIDISV 180
           N G     HP Q L D +TI+ R+G +   R    GD   + V  S +    A+  ++ V
Sbjct: 144 NAGDGSHEHPTQALLDALTIRRRRGSIAHQRVVICGDILHSRVARSNILALTALAAEVRV 203

Query: 181 ATPAVFRPIPGVVDKCRESIDVKLTTDPAEAAAGADIVFTDTFASIHNMDKER------- 233
             P+   P         E + V   TD   A  GAD+V       +  +  ER       
Sbjct: 204 VAPSTLMP------AAIEKMGVTPYTDFDAALEGADVVM------MLRLQNERMSGAYIP 251

Query: 234 -ERKFLPKYRVNAPLMKKAADDAIFMHCLPAKRGQEVDGEVIDGP-QSAVWDEAE 286
             R++   Y +    +K+A  DA+ MH  P  RG E+D  V D P +SA+ ++ E
Sbjct: 252 STREYHLNYGLTEERLKRAKPDALVMHPGPMNRGVEIDSSVADMPGRSAITEQVE 306


Lambda     K      H
   0.320    0.137    0.398 

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: 220
Number of extensions: 12
Number of successful extensions: 4
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: 301
Length of database: 330
Length adjustment: 27
Effective length of query: 274
Effective length of database: 303
Effective search space:    83022
Effective search space used:    83022
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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