GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Sinorhizobium meliloti 1021

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate SMc01360 SMc01360 aspartate carbamoyltransferase catalytic subunit

Query= curated2:P18186
         (319 letters)



>FitnessBrowser__Smeli:SMc01360
          Length = 313

 Score =  115 bits (289), Expect = 1e-30
 Identities = 94/316 (29%), Positives = 150/316 (47%), Gaps = 35/316 (11%)

Query: 12  KDLLTLKDLSEEDINALLAEAGEL-----KQNKIQPIFHGKTLAMIFEKSSTRTRVSFEA 66
           + LL +K L+E+DI  LL  A E      ++ K      G T   +F ++STRT+ SFE 
Sbjct: 7   RHLLGIKGLTEQDITLLLDRADEAVKISRQREKKTSSLRGLTQINLFFEASTRTQSSFEL 66

Query: 67  GMAQLGGSALFLSQKDLQLGRGETVADTAKVLSG-YVDAIMIRTFEHEKVEELAKEADIP 125
              +LG   + +S  +  + +GET+ DTA  L+  + D +++R         LA++    
Sbjct: 67  AGKRLGADVMNMSVGNSSVKKGETLIDTAMTLNAMHPDVLVVRHSSAGAASLLAQKVSCS 126

Query: 126 VINGLTDKY-HPCQALADLLTIKEIKGKLKGVKVAYIGD--GNNVAHSLMIGCAKMGCDI 182
           V+N    ++ HP QAL D LTI+  KGKL  + VA  GD   + VA S ++   +MG  +
Sbjct: 127 VVNAGDGQHEHPTQALLDALTIRRAKGKLSRIIVAICGDVLHSRVARSNILLLNQMGARV 186

Query: 183 SIASPKGYEVLDEAAEAAKTYALQSGSSVTLTDDPIEAVKDADVIYSDVFTSMGQEAEEQ 242
            + +P        A   A+ Y   +           E +KDADV+       M    + +
Sbjct: 187 RVVAPATLLPAGIAEMGAEVYHSMA-----------EGLKDADVV-------MMLRLQRE 228

Query: 243 ERLAVFAP--------YQVNAALVSHAKPDYTFLHCLPAHREEEVTAEIIDGPNSAVFQQ 294
                F P        Y ++A  +  AK D   +H  P +R  E+ +EI DGP S + QQ
Sbjct: 229 RMAGSFVPSVREYFHYYGLDAEKLKVAKDDALVMHPGPMNRGVEIASEIADGPQSVIEQQ 288

Query: 295 AENRLHVQKALLKAIL 310
            E  + V+ A+++ +L
Sbjct: 289 VEMGVAVRMAVMETLL 304


Lambda     K      H
   0.315    0.131    0.361 

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: 228
Number of extensions: 13
Number of successful extensions: 3
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: 319
Length of database: 313
Length adjustment: 27
Effective length of query: 292
Effective length of database: 286
Effective search space:    83512
Effective search space used:    83512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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