GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Pseudomonas fluorescens FW300-N2E2

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate Pf6N2E2_4606 Aspartate carbamoyltransferase (EC 2.1.3.2)

Query= curated2:Q2G3J8
         (311 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4606
          Length = 334

 Score =  115 bits (288), Expect = 1e-30
 Identities = 93/313 (29%), Positives = 150/313 (47%), Gaps = 28/313 (8%)

Query: 5   LKHFLNLTDAGGDAIAAMLNDALDRKSARAGQPKGKADADAPL-GGRVLAMVFEKNSTRT 63
           L+HFL+L     + +  +L+ A       A     +A    PL  G+ +  VF +NSTRT
Sbjct: 18  LRHFLSLDGLRRELLTEILDTADSFLEVGA-----RAVKKVPLLRGKTVCNVFFENSTRT 72

Query: 64  RVSFDIAMRQLGGSALILDAGTTQLGRGETIADTARVLSRM-ADAIMLRTDDHAKVEELA 122
           R +F++A ++L    + L+  T+   +GET+ DT R L  M AD  ++R  D      +A
Sbjct: 73  RTTFELAAQRLSADVITLNVSTSSASKGETLLDTLRNLEAMAADMFVVRHGDSGAAHFIA 132

Query: 123 RHA--TVPVINGLTDL-SHPCQIMADLLTVIEHGKALPGLEVAWLGDGNNVLNSIVEAAG 179
            H    V +ING     +HP Q M D+LT+  H  +   L VA +GD   +L+S V  + 
Sbjct: 133 EHVCPQVAIINGGDGRHAHPTQGMLDMLTIRRHKGSFENLSVAIVGD---ILHSRVARSN 189

Query: 180 LMKFNVRIGVPEGYESDAGMIEAAVLAGAGIRVIRDPVEAVRGADVVVTDTWISMGQAHA 239
           ++     +G P+        +    +   G++V  D  E ++  DVV+      M +   
Sbjct: 190 MLALKT-LGCPDIRVIAPKTLLPIGVEQYGVKVYTDMTEGLKDVDVVI------MLRLQR 242

Query: 240 EAKLAAMAP--------YQVNDALMAHAKPDAVFLHCLPAHRGEEVTDAVIDGPRSVVWD 291
           E     + P        + +  A +A AKPDA+ +H  P +RG E+  AV DGP SV+ +
Sbjct: 243 ERMTGGLLPSEGEFYRLFGLTTARLAGAKPDAIVMHPGPINRGVEIESAVADGPHSVILN 302

Query: 292 EAENRIHAQKSVL 304
           +    I  + +VL
Sbjct: 303 QVTYGIAIRMAVL 315


Lambda     K      H
   0.319    0.133    0.387 

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: 230
Number of extensions: 16
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: 311
Length of database: 334
Length adjustment: 28
Effective length of query: 283
Effective length of database: 306
Effective search space:    86598
Effective search space used:    86598
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